Recently in Biological complexity Category

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.

As a last treat for the 150^th 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.

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.

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.

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…

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.

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.

The New York Times’s science pages discuss a research study of Tiktaalik. The study in question has been published in the Journal Nature (1)

It was Neil Shubin’s team that found the Tiktaalik, as they had predicted.

Dr. Shubin said Tiktaalik was “still on the fish end of things, but it neatly fills a morphological gap and helps to resolve the relative timing of this complex transition.”

For example, fish have no neck but “we see a mobile neck developing for the first time in Tiktaalik,” Dr. Shubin said.

In previous essays (here and here), we learned that genes encoding new proteins can and do, often, arise de novo in the course of evolution, contradicting one of the central tenets of ID proponents. The means by which these genes arise are many. One of these, suggested by Cai at al. (the subject of one of the earlier essays), involved the adaptation of a gene encoding an evolutionarily-conserved non-coding RNA via the appearance, by mutation, of appropriate translation initiation and termination (“start” and “stop”) codons. This mechanism represents an intersection of sorts between the subject of protein evolution and another matter of discussion on these blogs, namely the existence, evolution, and “function” of junk DNA. In this essay, I review a 2007 study by Debrah Thompson and Roy Parker (“Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae”, Mol. Cell. Biol. 27, 92-101) that adds a great deal of clarity to this mode of gene and protein evolution.

Anne Minard of National Geographic News writes on July 9^th

The discovery of a missing link in the evolution of bizarre flatfishes—each of which has both eyes on the same side of its head—could give intelligent design advocates a sinking feeling.

CT scans of 50-million-year-old fossils have revealed an intermediate species between primitive flatfishes (with eyes on both sides of their heads) and the modern, lopsided versions, which include sole, flounder, and halibut.

So the change happened gradually, in a way consistent with evolution via natural selection—not suddenly, as researchers once had little choice but to believe, the authors of the new study say. … Though known for their odd eye arrangement, no flatfish start life that way. Each is born symmetrical, with one eye on each side of its skull.

As a flatfish develops from a larva to a juvenile, one eye migrates up and over the top of the head, coming to rest in its adult position on the opposite side of the skull. … Palmer added that the new work is “a fantastic paper” that helps resolve a mystery “that’s bedeviled evolutionary biologists for more than a century.

“It’s really been a major, major puzzle to evolutionary biologists.”

As expected, the Magisterium of Intelligent Design was quick to condemn the finding as simply floundering around, while the Institute of Creation Research has a turbot-charged attack on the finding, pointing out that flatfish are sole-ly members of the flatfish ‘kind,’ and putting National Geographic in it’s plaice.

Recently, we learned of an instance of the de novo origination of a new protein-coding gene in yeasts. This instance involved a mechanism or pathway that seems difficult to some, namely the random appearance of an open reading frame in an otherwise noncoding segment of DNA via judicious appearance of translation start and stop codons. The question naturally arises as to the relevance of such a pathway to real-life biology; was/is this a rather rare event that doesn’t really contribute to protein evolution, or is it a common means by which the protein-coding capacity of a genome is augmented?

A paper that is in press in Genome Research (Zhou et al., “On the origin of new genes in Drosophila”) gives us some insight into this question. The abstract of this paper summarizes things as well as I can:

A recurrent theme amongst ID proponents is the supposed difficulty of protein evolution, especially as it relates to the origination of new protein-coding genes. This is, I suspect, a key reason why ID proponents such as Paul Nelson are so enamoured of ORFans, and a foundational principle for the application of ID theory to evolution (the idea being that protein-coding genes are possessed of Complex Specified Information, and thus cannot arise by natural processes). Thus, studies that pertain to the origins of new protein-coding genes are going to factor largely in the scientific aspect of the ID debate, especially since ID proponents insist that new protein-coding genes cannot arise “by chance”.

It is in this context that a recent study by Jing Cai and colleagues is of interest. The title of the article suffices to explain the study – “De novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae”. What these authors describe is a series of studies of a yeast gene, BSC4. This gene was originally identified as a candidate containing a so-called read-through translation termination (or stop) codon. This gene was studied in more depth, whereupon Cai et al. found that the protein encoded by this gene was novel in genome databases, not resembling any other protein in any organism. Importantly, this includes the genomes of related Saccharomyces species; this indicates that this protein in S. cerevisiae arose relatively recently, after this species diverged from its close relatives.

I happened to read PZ’s write-up Local Boy Gets Obnoxious, in which he mentions how he has been interviewed by the Seattle-PI. If I had known PZ was in town, I would have attended the Pacific Science Center talk. Instead I ended up at a Seattle Skeptics “An Evening with PZ MYERS” event. This well attended meetup included a fascinating lecture about the evolution of the eye and introduced me to several aspects of eye evolution with which I had not been familiar.

The PT Crew received an email, announcing a breathtaking website called Exploring Life’s Origins. The website displays in stunning graphics and video how scientists are exploring the origins of life. The graphics were made by an NSF Discovery Corps Postdoctoral Fellow named Janet Iwasa, in collaboration with Jack Szostak, and the Current Science and Technology team at the Museum of Science, under an NSF grant. The resources are available under a Creative Commons License which requires attribution, non-commercial use and no derivative works. The website explains in clear and accessible language how science envisions life arose on earth and explains the RNA world, which, despite the wishful thinking of some creationists, has not lost its relevance.

Michael Le Page at New Scientist discusses Evolution: 24 myths and misconceptions.

Shared misconceptions:

Everything is an adaptation produced by natural selection
Natural selection is the only means of evolution
Natural selection leads to ever-greater complexity
Evolution produces creatures perfectly adapted to their environment
Evolution always promotes the survival of species
It doesn’t matter if people do not understand evolution
“Survival of the fittest” justifies “everyone for themselves”
Evolution is limitlessly creative
Evolution cannot explain traits such as homosexuality
Creationism provides a coherent alternative to evolution

Read on for the much longer list of Creationist myths

Hearts come in a variety of shapes and forms all the way from single chambered hearts to multi-chambered hearts with 2, 3 and even 4 separate chambers. How could evolution have achieved such a feat one may wonder, and indeed creationists have held up this minor mystery as something evolutionary theory could and would never be able to explain.

As is so often the case with such gap arguments, science has not failed to disappoint our creationist friends.

Science Daily gives us a hint of what science has uncovered in an article called Hearts Or Tails? Genetics Of Multi-chambered Heart Evolution

The expanded cardiac field in Ets1/2-activated mutants results in a proportion of animals having a functional, two-chambered heart. “The conversion of a simple heart tube into a complex heart was discovered by chance, but has general implications for the evolutionary origins of animal diversity and complexity”, says Mike Levine, a co-author of the paper.