Recently in Biological complexity Category

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.

The evolution of the blowhole in whales, which according to the fossil evidence moved from the tip to the vertex of the head, has caused some concerns amongst our creationist readers who wonder how such a feat could have taken place.

From Milan Klima, Development of the Cetacean Nasal Skull 1999 Springer

The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment. To a certain extent, cetaceans can be considered to be the most successful group of aquatic animals of all time.

Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlager 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kukenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostra tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages. At the same time, a long rost rum with narrow jaws develops. Until recently, practically nothing was known about the morphogenetic processes concealed in this metamorphosis, about what cranial structures take part in it, and about the exact way in which the cetacean skull becomes transformed during embryogeny.

The University of California, San Diego (UCSD), the alma mater of Discovery Institute’s spokesperson Casey Luskin, explores why “Evolution Matters”. In cooperation with UCSD-TV, they bring us a fascinating lecture series:

For 2007-08, the Division of Biological Sciences is launching Evolution Matters: The Diversity of Development. In this series of 5 lectures, held over the course of the year, leading cell and developmental scientists will explore the evolution of plants, animals and humans and will discuss how their research into this field holds promise for finding solutions to key health and environmental issues facing us today.

Educational Website: Grey Matters

Educational Website: Science Matters

Atoms to Xrays

Neil Shubin’s latest book on evolutionary theory is by all standards a great success. It ranks around 200 in Amazon books and first in Evolution Science Books. When I checked the book’s availability in our library system there were close to 40 pending holds.

A sales rank of 200 means 225-250 books per week are sold. Compare this to a rank of 24,000 for Behe’s boo “Edge of Evolution” sold at a bargain price of $6.99 down from $28.00 or 111,550 for the regular priced version. Those numbers translate to few copies per month being sold.

Neil Shubin is a professor of organismal biology at the University of Chicago. He, as part of a team of scientists, discovered the now infamous Titaalik transitional fossil which causes so much consternation amongst Intelligent Design Creationists. His book Your Inner Fish introduces its readers to an exciting overview of how our evolutionary history links us back to a common ancestor with fish. Of course, that’s not where our common ancestry ends.

Why do we look the way we do? What does the human hand have in common with the wing of a fly? Are breasts, sweat glands, and scales connected in some way? To better understand the inner workings of our bodies and to trace the origins of many of today’s most common diseases, we have to turn to unexpected sources: worms, flies, and even fish.

In Your Inner Fish, Neil Shubin tells the story of evolution by tracing the organs of the human body back millions of years, long before the first creatures walked the earth. By examining fossils and DNA, Shubin shows us that our hands actually resemble fish fins, our head is organized like that of a long-extinct jawless fish, and major parts of our genome look and function like those of worms and bacteria.

Yesterday a really cool paper came out in the journal Nature that demonstrates why evolutionary theory is so useful and fruitful in biology. A team of researchers has recreated an ancestral bacterial protein to determine that the ancestral bacteria grew in hot water around 3.5 billion years ago.

The Union of Concerned Scientists has released a six section overview on Science, Evolution, and Intelligent Design

Section 1: Science as a Way of Knowing
Section 2: Science and Society
Section 3: Evolution, Creationism, and Intelligent Design
Section 4: Why Intelligent Design is not Science
Section 5: Science Education and Intelligent Design
Section 6: Fairness and Balance in the Classroom and Beyond

I would add another section on the scientific vacuity or infertility of Intelligent Design. Ask yourself this simple question: What non-trivial contribution has Intelligent Design made to our scientific understanding? And ask you then a follow-up question: For those systems which ID claims to be designed, how does ID explain these systems?

The answers, or lack thereof, may surprise you.

HT: NCSE

The New York Academy of Sciences provides us with access to a talk by Nobel Laureate Christiane Nüsslein-Volhard on how genes drive development, no need for unspecified ‘Intelligent Designers’, no need for miracles, just hard work by scientists who are committed to discovering the details of how, what, when and so on. Compare this with how ID explains the development of the embryo.

Click on the Flash presentation

I also suggest that interested readers get their hands on her book “Coming to Life: How Genes Drive Development” by Christiane Nüsslein-Volhard or read an excerpt of the book: Chapter IX — Evolution, Body Plans, and Genomes

We are all familiar with the creationist argument about the eye, an argument which Darwin already addressed in his original work. And while creationists are still in much of a denial about eye evolution, science keeps on closing gaps.

In the Australian a second paper addressing eye evolution is discussed.

Laurence Moran at Sandwalk comments on a video excerpt with Bill Dembski, recently touted by the Discovery Institute’s Robert Crowther. What is fascinating that despite more than a decade of Intelligent Design ‘research’ this is the best ID has to offer.

Ironically, Dembski starts of by stating that “what darwinists have done is hidden behind complexities of living systems”. How ironic can this be… While science, as I have shown in several examples, deals in explanations, pathways and hypotheses, Intelligent Design has contributed exactly zero to our scientific understanding of these systems. Worse, while Dembski mentions some complex systems, he also avoids some examples of complex systems science understands quite well how they may have evolved.

My thanks to Robert Crowther for presenting the “best’ response ID has to offer. You be the judge.

The Seattle Times has an interesting article on the link between political views and the brain

In a study likely to raise the hackles of some conservatives, scientists at New York University and the University of California, Los Angeles, found that a specific region of the brain’s cortex is more sensitive in people who consider themselves liberals than in self-declared conservatives.

Based on the findings we can make some predictions

Based on the results, Sulloway said, liberals could be expected to more readily accept new social, scientific or religious ideas.

Or alternatively, conservatives will be less ready to accept new scientific ideas.

Imagine that

Well now we understand

Analyzing the data, Sulloway said liberals were 4.9 times more likely than conservatives to show activity in the brain circuits that deal with conflicts and were 2.2 times more likely to score in the top half of the distribution for accuracy.

A recent paper (free access) by Associate Professor Susan Dudley, published in the Royal Society journal Biology Letters argues that some plants recognize their kin.

Kin recognition is important in animal social systems. However, though plants often compete with kin, there has been as yet no direct evidence that plants recognize kin in competitive interactions. Here we show in the annual plant Cakile edentula, allocation to roots increased when groups of strangers shared a common pot, but not when groups of siblings shared a pot. Our results demonstrate that plants can discriminate kin in competitive interactions and indicate that the root interactions may provide the cue for kin recognition. Because greater root allocation is argued to increase below-ground competitive ability, the results are consistent with kin selection.

Although it were gardeners who knew this all along:

There has been a spate of interest in the blogosphere recently in the matter of protein evolution, and in particular the proposition that new protein function can evolve. Nick Matzke summarized a review (reference 1) on the subject here. Briefly, the various mechanisms discussed in the review include exon shuffling, gene duplication, retroposition, recruitment of mobile element sequences, lateral gene transfer, gene fusion, and de novo origination. Of all of these, the mechanism that received the least attention was the last – the de novo appearance of new protein-coding genes basically “from scratch”. A few examples are mentioned (such as antifreeze proteins, or AFGPs), and long-time followers of ev/cre discussions will recognize the players. However, what I would argue is the most impressive of such examples is not mentioned by Long et al. (1). Below the fold, I will describe an example of de novo appearance of a new protein-coding gene that should open one’s eyes as to the reach of evolutionary processes. To get readers to actually read below the fold, I’ll summarize – what we will learn of is a protein that is not merely a “simple” binding protein, or one with some novel physicochemical properties (like the AFGPs), but rather a gated ion channel. Specifically, a multimeric complex that: 1. permits passage of ions through membranes; 2. and binds a “trigger” that causes the gate to open (from what is otherwise a “closed” state). Recalling that Behe, in Darwin’s Black Box, explicitly calls gated ion channels IC systems, what the following amounts to is an example of the de novo appearance of a multifunctional, IC system.

Douglas Axe recently (well, sort of) published an article in the Journal of Molecular Biology entitled “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” (Axe, J Mol Biol 341, 1295-1315, 2004). In his discussion of the experimental observations, Dr. Axe mentions some numbers that are likely to generate much discussion amongst Intelligent Design advocates and critics. For example, Stephen Meyer (2004) cites Axe at a key point in the argument in his recent article advocating Intelligent Design, “The Origin of Biological Information and the Higher Taxonomic Categories,” much discussed in previous Panda’s Thumb threads (here).

“Axe (2004) has performed site directed mutagenesis experiments on a 150-residue protein-folding domain within a B-lactamase enzyme. His experimental method improves upon earlier mutagenesis techniques and corrects for several sources of possible estimation error inherent in them. On the basis of these experiments, Axe has estimated the ratio of (a) proteins of typical size (150 residues) that perform a specified function via any folded structure to (b) the whole set of possible amino acids sequences of that size. Based on his experiments, Axe has estimated his ratio to be 1 to 10^77. Thus, the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.”

More recently, Dembski cited Axe in his Expert Witness Report for the Dover trial (see this).

“Recent research by Douglas Axe (see Appendix 3) provides such evidence in the form of a rigorous experimental assessment of the rarity of function-bearing protein sequences. By addressing this problem at the level of single protein molecules, this work provides an empirical basis for deeming functional proteins and systems of functional proteins to be unequivocally beyond Darwinian explanation.”

Given that this subject is often raised by ID proponents (such as this), and that the Biologic Institute (where Axe works) has made some news accounts, it seems appropriate to review Axe’s work. The purpose of this PT blog entry is to try and lay out the study cited above (Axe DD, J Mol Biol 341, 1295-1315, 2004) in a form that is accessible to most interested parties, and to discuss a larger context into which this work might be placed. Needless to say, the grand pronouncements being made by the ID camp are not warranted.

PNAS has published an article by Soyer and BonHoeffer titled Evolution of complexity in signaling pathways

Abstract: It is not clear how biological pathways evolve to mediate a certain physiological response and why they show a level of complexity that is generally above the minimum required to achieve such a response. One possibility is that pathway complexity increases due to the nature of evolutionary mechanisms. Here, we analyze this possibility by using mathematical models of biological pathways and evolutionary simulations. Starting with a population of small pathways of three proteins, we let the population evolve with mutations that affect pathway structure through duplication or deletion of existing proteins, deletion or creation of interactions among them, or addition of new proteins. Our simulations show that such mutational events, coupled with a selective pressure, leads to growth of pathways. These results indicate that pathways could be driven toward complexity via simple evolutionary mechanisms and that complexity can arise without any specific selective pressure for it. Furthermore, we find that the level of complexity that pathways evolve toward depends on the selection criteria. In general, we find that final pathway size tends to be lower when pathways evolve under stringent selection criteria. This leads to the counterintuitive conclusion that simple response requirements on a pathway would facilitate its evolution toward higher complexity.

Read on for some of my thoughts.

Students are often overwhelmed by the number of species concepts cited in the literature. Here is a working list of species concepts presently in play. I quote “Concepts” above because, for philosophical reasons, I think there is only one concept - “species”, and all the rest are conceptions, or definitions, of that concept. I have christened this the Synapormorphic Concept of Species in (Wilkins 2003).

Read the rest on Evolving Thoughts.

Anyone who has been a “creationism watcher” for any length of time is familiar with the venerable creationist tactic of “quote mining.” Since creationists, essentially universally, can’t (or don’t want to) deal with actual scientific data pertaining to evolution, they attempt maintain a facade of respectibility by quoting statements from biological authorities. This can take many forms; for example, for the 1987 Supreme Court Edwards v. Aguillard case, the creationist lawyer Wendell Bird, apparently with the help of Paul Nelson, assembled a massive 500-page brief that consisted almost entirely of thousands of quotes from authorities on every topic bearing on “creation science”, from astrophysics to biology to philosophy to religion. This failed to convince the Supremes, but Bird turned his brief into a large two-volume book, The Origin of Species Revisited. Other elaborations on creationist quote-mining include various “Quote Books”, including The Quote Book (1984 booklet, inserted in Creation magazine I believe) and The Revised Quote Book (1990) from Answers in Genesis, the Handy Dandy Evolution Refuter (now online), and Henry Morris’ That Their Words may be used against Them (comes with CD!). Then we have endless collections of quotes on creationist websites, 50 of which were recently surveyed and ranked against the Talk.Origins Quote-Mine Project. Sometimes these quotes evolve and mutate over time (here is an example from Of Pandas and People), and sometimes they even spontaneously generate from thin air, as with this imaginary quote from Clarence Darrow.

You may be saying, “Surely this is a problem, but only famous authorities get quote mined. It would never happen to me!” Think again. On September 5, 2006, an article I coauthored in Nature Reviews Microbiology on flagellum evolution was published on the NRM website as an Advanced Online Publication. Before the ink was even dry – heck, before the ink was even wet, the October issue hasn’t come out yet – Casey Luskin at the Discovery Institute is quote mining it! The mining occured in Luskin’s insta-response to the revised edition Chris Mooney‘s book The Republican War on Science. Check this out:

A paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

Genetic Algorithms are simplified simulations of evolution that often produce surprising and useful answers in their own right. Creationists and Intelligent Design proponents often criticize such algorithms for not generating true novelty, and claim that these mathematical recipes always sneak the “answer” into the program via the algorithm’s fitness testing functions.

There’s a little problem with this claim, however. While some Genetic Algorithms, such as Richard Dawkin’s “Weasel” simulation, or the “Hello World” genetic algorithm discussed a few days ago on the Thumb, indeed include a precise description of the intended “Target” during “fitness testing” on of the numerical organisms being bred by the programmer, such precise specifications are normally only used for tutorial demonstrations rather than generation of true novelty.

In this post, I will present my research on a Genetic Algorithm I developed a few years ago, for the specific purpose of addressing the question Can Genetic Algorithms Succeed Without Precise “Targets”? For this investigation, I picked a math problem for which there is a single, specific answer, yet one for which several interesting “quasi-answers” - multiple “targets” - also exist.

PT readers, you are about to enter the Strange and Curious world of “The MacGyvers.” Buckle up your seat belts, folks - our ride through Fitness Landscapes could get a little bumpy.

So, archaea are apparently the topic of the week. While I wrote here about the pathogenic potential of some species of these organisms, a new essay in Nature and a new review in Science focus more on their evolution (and the evolution of the other two domains of life) than any health application.

In the essay mentioned, Norman Pace discusses the eukaryote/prokaryote dichotomy. Currently the archaea are classified as prokaryotes since they, like bacteria, lack a true nucleus. However, molecular sequence analysis has shown that the archaea and eukaryotes are actually more closely related to each other than either group is to bacteria (see figure, from Pace’s Nature essay). As such, nomenclature that places the bacteria and archaea together into a group is misleading.

(Continued at Aetiology)

The evolution of cooperation has long been a vexing problem in biology. In the 1960s and later, a number of proposals to account for various forms of cooperation were offered, including group selection, kin selection, and reciprocal altruism. Both kin selection and reciprocal altruism have some biological data to which to appeal. In The Selfish Gene Dawkins argued that cooperative behavior could emerge as ‘selfish’ genes evolved in the context of other genes (indeed, he’s said that the book could have been title The Cooperative Gene with no change in content) and to the extent that cooperation is an effective strategy for gene vehicles (organisms) to increase reproductive success, but that was largely a formal argument rather than an empirical one. And group selection (which Dawkins emphatically rejects), in my view at least is still on shaky empirical grounds. (Apologies to Steve Rissing, a friend and Project Steve Steve with whom I argue about that.)

A difficulty of doing research on cooperation is the same difficulty that plagues much research on other complex evolutionary phenomena, namely time: interesting multi-celled animals have (relatively) long lifetimes and following a population for many generations is impossible for a single researcher.

Enter computer models. I will not here rehearse the history of computer modeling of evolutionary processes, since I’ve previously touched on it here, here and here on PT.

Of present interest is a study of the evolution of cooperation in a computer model of evolution. Prior work has shown that there are conditions in which several kinds of ‘strategies’ for interactions among artificial agents can evolve. Robert Axelrod, for example, has done a slew of work on that topic. Game theory informs much of that research, and has been useful in predicting the occurrence of certain kinds of strategies in multi-agent contexts.

A new study by Mikhail Burtsev & Peter Turchin (Nature, 440:1041-1044, April 2006) provides a good deal more insight into how cooperative strategies can evolve.

More below the fold.

IBM researchers have shown how science explores new and innovative approaches to discover DNA patterns which are shared by areas of the human genome that were considered to have little or no influence on its function and areas which do have function.

From the IBM Press Release

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

Two threads combine in this posting. First my comments on the Beckwith thread where I show how Dembski and Behe use the term specification or purpose to refer to “function”, and secondly a thread on strings in which the concept of purpose arose again.

First let’s revisit Dembski’s and Behe’s position on function which shows that their use of the term specification or purpose clearly refers to function.

van Till Wrote:

However, when it comes time for Dembski to support his conviction that the bacterial flagellum is specified, the procedure becomes considerably more casual, almost facile. Speaking on the specification of biological systems in general, Dembski simply asserts that, “Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specification criterion.”NFL, p. 148.In these four brief sentences the foundation of Dembski’s entire strategy for certifying the specification of biotic systems is laid.

Or in Behe’s terms “a purposeful arrangement of parts” where purpose and function are interchangeable.

Behe Wrote:

Q The whole positive argument for intelligent design as you ve described it, Professor Behe, is look at this system, look at these parts, they appear designed correct?

A Well, I think I filled that out a little bit more. I said that intelligent design is perceived as the purposeful arrangement of parts, yes. So when we not only see different parts, but we also see that they are ordered to perform some function, yes, that is how we perceived design.

Page 44 of Behe’s cross examination on Day 11 of the Kitzmiller trial. See also Analysis of Behe’s Testimony, Part 1: Purpose and Function at “Dispatches from the Culture Wars”

Although I hate to give credibility to statements which are so anti-science, I also believe that educating those who are willing to hear the “rest of the story” is important.

Point in case:

In a recent blog posting, Denyse O’Leary stated the following on the Cambrian explosion. Since her comments may be of direct interest to this group, I would like to repeat them here and discuss why they are flawed.

For Neurode…

Bergstrom (Department of Zoology University of Washington Seattle, WA, USA) and Lachmann (Max Planck Institute for Mathematics in the Sciences Leipzig, Germany) have published a paper titled “Shannon Information and Biological Fitness”.

They conclude that

In this paper we have shown that two measures of information, Shannon entropy and the decision-theory value of information, are united into one single information measure when one looks at the strategies that natural selection will favor, namely those that maximize the long term growth rate of biological organisms. Furthermore, we have shown that in evolving biological systems, the fitness value of information is bounded above by the Shannon entropy. These results suggest a close relationship between biological concepts of Darwinian fitness and information-theoretic measures such as Shannon entropy or mutual information.

Carl Zimmer on “The Loom” describes recent work on the phylogenetic tree. Researchers have looked at vertical and horizontal transmission of genetic information in various bacteria.

I would like to focus on a particular aspect of the findings, namely the [u]scale free[/u] nature of the horizontal gene transfer networks. People may remember the scale free networks in RNA for instance and how such networks have some very important properties. Scale free networks can be explained through the simple process of duplication and preferential attachment. In this case, the researchers showed that the horizontal ‘vines’ of the tree form scale free networks.

So what?