Recently in Biological complexity Category

Report on a Creation Evidence Expo

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On Biodork there’s a guest post reporting a visit by several skeptics/atheists to a Creation “Evidence” Expo held recently in Indianapolis. A couple of excerpts to entice you to read it all:

It turns out creationism is still alive and kicking. Okay, maybe not kicking so much as floundering so it doesn’t drown.

Of some note, creationists have already picked up the ENCODE project’s “80% of the genome is functional” meme that’s polluting mainstream media and the blogosphere. (See T. Ryan Gregory for a representative critique of the PR misrepresentations of the ENCODE papers, and Nature News for an overview of some of the critiques. And here’s Nature’s portal to the ENCODE data.) At the Creation “Evidence” Expo YEC Nuclear chemist Dr. Jay Wile is reported to have used ENCODE’s bogus ‘80% functional’ claim:

He began quoting biology books from 1989 and talking about “junk DNA”. He informed the audience that junk DNA doesn’t exist because god made us and that they now know 80% of what our DNA does.

Ewan Birney, lead coordinator of ENCODE, has a lot to answer for.

The ENCODE delusion

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I can take it no more. I wanted to dig deeper into the good stuff done by the ENCODE consortium, and have been working my way through some of the papers (not an easy thing, either: I have a very high workload this term), but then I saw this declaration from the Electronic Frontier Foundation.

On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California's warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

I've been guilty of teaching bean-bag genetics this semester. Bean-bag genetics treats individuals as a bag of irrelevant shape containing a collection of alleles (the "beans") that are sorted and disseminated by the rules of Mendel, and at its worst, assigns one trait to one allele; it's highly unrealistic. In my defense, it was necessary — first-year students struggle enough with the basic logic of elementary transmission genetics without adding great complications — and of course, in some contexts, such as population genetics, it is a useful simplification. It's just anathema to anyone more interested in the physiological and developmental side of genetics.

The heart of the problem is that it ignores the issue of translating genotype into phenotype. If you've ever had a basic genetics course, it's quite common to have been taught only one concept about the phenotype problem: that an allele is either dominant, in which case it is expressed as the phenotype, or it's recessive, in which case it is completely ignored unless it's the only allele present. This idea is so 19th century — it's an approximation made in the complete absence of any knowledge of the nature of genes.

Oh no! It’s Granville Sewell again. At Uncommon Descent he has posted his 2nd law of thermodynamics argument against evolution, yet again. I have twice pointed out that (here and here) that, if true, it would prove that plants can’t grow.

Is Sewell’s argument unanswerable? No, because long before I made those posts, Sewell’s argument had been thoroughly demolished by Jason Rosenhouse and by Mark Perakh. Game over, even if you don’t know that plants can grow.

But Granville Sewell’s argument over at Uncommon Descent is unanswerable. At least there … because he has the comments turned off.

[Review of Shapiro, James A. Evolution: A View from the 21st Century. FT Press Science, ISBN: 0-13-278093-3, $34.99 Publisher’s site]

Over the years there have been many books that purport to “radically revise” or “supplant” Darwinian evolutionary biology; they come with predictable regularity. Usually they are of three kinds: something is wrong with natural selection, something is wrong with inheritance, or something is wrong with phylogeny. This book, by geneticist James A. Shapiro, exemplifies all three.

It is of course a cliche to state that eukaryotic cells (i.e., cells that are not bacteria) are complex. In the case of an animal, tens of thousands of proteins engage in fantastically elaborate interactions that somehow coax a single cell into generating a unique and magnificent organism. These interactions are often protrayed as exquisitely precise, using metaphorical images such as ‘lock-and-key’ and employing diagrams that resemble subway maps.

Many of these interacting proteins are enzymes that modify other proteins, and many of those enzymes are of a particular type called kinases. Kinases do just one thing: they attach phosphate groups to other molecules. This kind of modification is centrally important in cell biology, and one way to tell is to look at how many kinases there are: the human genome contains about 500 kinase genes.

Now, kinases tend to be pretty picky about who they stick phosphate onto, and this specificity is known to involve the business end of the kinase, called the active site. The active site is (generally) the part of the kinase that physically interacts with the target and transfers the phosphate. You might think that this interaction, between kinase and target, through the active site, would be by far the most important factor in determining the specificity of kinase function. But that’s probably not the case.

How to afford a big sloppy genome

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My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I've come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we'd extract embryos from their eggs, and we'd keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I'd put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant's causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn't obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that's no moon. It's a multicellular organism.

This week’s issue of Science has a news article and a podcast about a USGS researcher who bred bacteria to live in an arsenic environment. If you do not subscribe to Science, you may read only slightly breathless articles in the New York Times and the Los Angeles Times.

Several years ago, I saw a fantastic talk at the Evolution meeting about Intraspecific macroevolution: variation of cranial shape in dog breeds. The talk was by Abby Drake, then a grad student, and reported on a huge digital morphometric comparison of the skulls of dogs and many representatives from the order Carnivora (dogs, cats, bears, sea lions, etc.).

Morphometrics basically consists of taking digital photos of e.g. bones from different angles, and then marking the same landmarks on homologous bones across a big group. Then you can quantitatively compare the differences in shape, independent of things like body size. This is a much more sophisticated analysis than is possible with just calipers, where you can only get length, width, etc.

No metazoan is an island

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I'm one of those dreadful animal-centric zoologically inclined biologists. Plants? What are those? Fungi? They're related to metazoans somehow. Lichens? Not even on the radar. The first step in fixing a problem, though, is recognizing that you have one. So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.

My path to opening up to wider horizons is to focus on what I find most interesting about animals, and that is that they are networks of cells driven by networks of genes that generate patterned responses of expression by cell signaling, or communication. See? I'm already a little weird. Show me a baby bunny, and I don't just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo. And ultimately, I want to take apart each cell and ask why it has its particular assortment of genes switched off and on, and how its state affects its neighbors and the whole of the organism.

Which means, lately, that I've acquired a growing interest in bacteria. If I were 30 years younger, I could probably be seduced into a career in microbiology.

There are a couple of reasons why an animal-centric biologist would be interested in bacteria. One is the principle of it; the mechanisms that animal cells use to build complex arrangements of tissues were all first pioneered in single-celled organisms. We have elaborated and added details to gene- and cell-level phenomena, but it's a collection of significant quantitative differences, with nothing known that is essentially new in metazoan cells. All the cool stuff was worked out by evolution in the 3-4billion years before the Cambrian, a potential that simply blossomed in the past half-billion years into big conglomerations of cells. Understanding how the building blocks of multicellularity work individually ought to be a prerequisite to understanding how the assemblages work.

But there's another reason, too, a difference in perspective. It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It's not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team. Genus Homo is also genera Escherichi and Bacteroidetes and Firmicutes and many others.

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PrimordialSoupPPR.jpg

Science Daily reports today that

For 80 years it has been accepted that early life began in a ‘primordial soup’ of organic molecules before evolving out of the oceans millions of years later. Today the ‘soup’ theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth’s chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

“Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP. We provide a new perspective on why that old and familiar view won’t work at all,” said team leader Dr Nick lane from University College London. “We present the alternative that life arose from gases (H2, CO2, N2, and H2S) and that the energy for first life came from harnessing geochemical gradients created by mother Earth at a special kind of deep-sea hydrothermal vent – one that is riddled with tiny interconnected compartments or pores.”

The soup theory was proposed in 1929 when J.B.S Haldane published his influential essay on the origin of life in which he argued that UV radiation provided the energy to convert methane, ammonia and water into the first organic compounds in the oceans of the early earth. However critics of the soup theory point out that there is no sustained driving force to make anything react; and without an energy source, life as we know it can’t exist. …

Discuss.

Hunter vs. Hunt on Turf-13

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As a last treat for the 150th anniversary of the Origin, have a look at young-earth creationist creationist Cornelius Hunter [Update: Hunter has stated he is not a young-earth creationist on his blog, so I guess he’s not, although that position directly follows from his stated theology/philosophy], author of the “Darwin’s God” book and blog. Hunter’s basic argument against virtually any common pro-evolution argument is, basically, “But you evolutionists are claiming that God wouldn’t have done it this way! You’re making an unscientific theological argument!”

Intelligent design creationists love to talk about information theory, but unfortunately they rarely understand it. Jonathan Wells is the latest ID creationist to demonstrate this.

In a recent post at “Evolution News & Views” describing an event at the University of Oklahoma, Wells said, “I replied that duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content.”

Wells is wrong. I frequently give this as an exercise in my classes at the University of Waterloo: Prove that if x is a string of symbols, then the Kolmogorov information in xx is greater than that in x for infinitely many strings x. Most of my students can do this one, but it looks like information expert Jonathan Wells can’t.

Like many incompetent people, Wells is blissfully unaware of his incompetence. He closes by saying, “Despite all their taxpayer-funded professors and museum exhibits, despite all their threats to dismantle us and expose us as retards, the Darwinists lost.”

We don’t have to “expose” the intelligent design creationists as buffoons; they do it themselves whenever they open their mouths.

A Paul Nelson Anniversary Missed!

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We missed an important anniversary last week. It was five years ago last Sunday, March 29, that Paul Nelson told us that he’d provide a reply to PZ Myers’ critique of “ontogenetic depth.” Nelson said

Quick note – I’m drafting an omnibus reply (to points raised here and in Shalizi’s commentary), with title and epigraph from a Rolling Stones song. I’ll post it tomorrow.

Yup. And the check’s in the mail, right? I suspect the epigraph should be “(I can’t get no) Satisfaction.”

By tradition the fifth anniversary of an event is the “wood” anniversary. But so far we don’t even have one wooden nickel from Paul, say nothing of an omnibus full of them. We’re still waiting, Paul.

Durston’s devious distortions

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A few people (actually, a lot of people) have written to me asking me to address Kirk Durston’s probability argument that supposedly makes evolution impossible. I’d love to. I actually prepared extensively to deal with it, since it’s the argument he almost always trots out to debate for intelligent design, but — and this is a key point — Durston didn’t discuss this stuff at all! He brought out a few of the slides very late in the debate when there was no time for me to refute them, but otherwise, he was relying entirely on vague arguments about a first cause, accusations of corruption against atheists, and very silly biblical nonsense about Jesus. So this really isn’t about revisiting the debate at all — this is the stuff Durston sensibly avoided bringing up in a confrontation with somebody who’d be able to see through his smokescreen.

If you want to see Durston’s argument, it’s on YouTube. I notice the clowns on Uncommon Descent are crowing that this is a triumphant victory, but note again — Durston did not give this argument at our debate. In a chance to confront a biologist with his claims, Durston tucked his tail between his legs and ran away.

Blogging on Peer-Reviewed Research

The intelligent design creationists are jubilant — a paper has been published that shows that organisms were front-loaded with genes for future function! It describes "'latent' or 'preexistent' evolutionary potential" in our history, they say.

One small problem. The paper says nothing of the kind. It does mention latent potential, but it means something entirely different from something that is 'front-loaded', which is a sneaky little elision on the part of the creationists. There isn't even the faintest whiff of a teleological proposal in the paper at all, which makes me wonder if they even read it, or if, as seems more likely, they're simply incapable of comprehending the scientific literature.

So let's take a look at what the paper is actually about, and you'll see that it in no way supports the self-serving cheering of the creationists.

Creationists think information theory poses a serious challenge to modern evolutionary biology – but that only goes to show that creationists are as ignorant of information theory as they are of biology.

Whenever a creationist brings up this argument, insist that they answer the following five questions. All five questions are based on the Kolmogorov interpretation of information theory. I like this version of information theory because (a) it does not depend on any hypothesized probability distribution (a frequent refuge of scoundrels) (b) the answers about how information can change when a string is changed are unambiguous and agreed upon by all mathematicians, allowing less wiggle room to weasel out of the inevitable conclusions, and (c ) it applies to discrete strings of symbols and hence corresponds well with DNA.

All five questions are completely elementary, and I ask these questions in an introduction to the theory of Kolmogorov information for undergraduates at Waterloo. My undergraduates can nearly always answer these questions correctly, but creationists usually cannot…

Evolution Education: Evolution of the Eye Special Issue

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One of our strategies in the defense of science and the Enlightenment (yes, Ken Miller’s Only a Theory is having an effect on me) has to be to increase the level of scientific knowledge among educators, especially secondary school teachers, and to show how much we actually know about how evolution works to produce complicated organs. One of the canonical complicated organs, the vertebrate eye, is a long-time favorite of creationists and IDists. They happily quote Darwin’s notorious introductory sentence about it:

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.

But then they ignore his answer to the problem in the next sentence:

Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real.

Now an outstanding resource to support evolutionary claims about eye evolution is available. A special issue of Evolution: Education and Outreach, which is under the general editorship of Gregory and Niles Eldredge, is available free online. The special issue was edited by T. Ryan Gregory, who also wrote the Introduction to the issue. It includes 11 articles of original research and reviews, three on curriculum possibilities, and a book review. All told it is an excellent resource.

Entropy and evolution

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One of the oldest canards in the creationists' book is the claim that evolution must be false because it violates the second law of thermodynamics, or the principle that, as they put it, everything must go from order to disorder. One of the more persistent perpetrators of this kind of sloppy thinking is Henry Morris, and few creationists today seem able to get beyond this error.

Remember this tendency from order to disorder applies to all real processes. Real processes include, of course, biological and geological processes, as well as chemical and physical processes. The interesting question is: "How does a real biological process, which goes from order to disorder, result in evolution. which goes from disorder to order?" Perhaps the evolutionist can ultimately find an answer to this question, but he at least should not ignore it, as most evolutionists do.

Especially is such a question vital, when we are thinking of evolution as a growth process on the grand scale from atom to Adam and from particle to people. This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

As most biologists get a fair amount of training in chemistry, I'm afraid he's wrong on one bit of slander there: we do not ignore entropy, and are in fact better informed on it than most creationists, as is clearly shown by their continued use of this bad argument. I usually rebut this claim about the second law in a qualitative way, and by example — it's obvious that the second law does not state that nothing can ever increase in order, but only that an decrease in one part must be accompanied by a greater increase in entropy in another. Two gametes, for instance, can fuse and begin a complicated process in development that represents a long-term local decrease in entropy, but at the same time that embryo is pumping heat out into its environment and increasing the entropy of the surrounding bit of the world.

It's a very bad argument they are making, but let's consider just the last sentence of the quote above.

This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

A "gigantic increase in order and complexity" … how interesting. How much of an increase? Can we get some numbers for that?

Information content of DNA

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The information content of DNA is much harder to determine than merely looking at the number of base pairs and multiplying it by 2 to get the size in bits (remember that each site can have up to 4 different nucleotides, or 2 bits). However, this approach can provide us with a zeroth order estimate of the maximum possible information that can be stored in said sequence which for the human genome with 3 billion base pairs would amount to 6 billion bits or 750 Mbytes.

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