eldavojohn writes: The global warming debate has left much to be desired in the realms of logic and rationale. One particular researcher, Michael E. Mann, has been repeatedly attacked for his now infamous (and peer reviewed/independently verified) hockey stick graph. It has come to the point that he is now suing for defamation over being compared to convicted serial child molester Jerry Sandusky. Articles hosted by defendants and written by defendant Rand Simberg and defendant Mark Steyn utilize questionable logic for implicating Michael E. Mann alongside Jerry Sandusky with the original piece concluding, 'Michael Mann, like Joe Paterno, was a rock star in the context of Penn State University, bringing in millions in research funding. The same university president who resigned in the wake of the Sandusky scandal was also the president when Mann was being (whitewashed) investigated. We saw what the university administration was willing to do to cover up heinous crimes, and even let them continue, rather than expose them. Should we suppose, in light of what we now know, they would do any less to hide academic and scientific misconduct, with so much at stake?' Additionally, sentences were stylized to blend the two people together, 'He has molested and tortured data in the service of politicized science that could have dire economic consequences for the nation and planet' and one of the defendants admits to removing "a sentence or two" of questionable wording. Still, as a public figure, Michael E. Mann has an uphill battle to prove defamation in court.
eldavojohn writes: A recent peer reviewed paper and survey by Cliff Frohlich, of the University of Texas' Institute for Geophysics, reveals a correlation between an increase in earthquakes and the emergence of fracking sites in the Barnett Shale, Texas. To clarify, it is not the actual act of hydrofracking that induces earthquakes but more likely the final process of injecting wastewater into the site according to Oliver Boyd, a USGS seismologist. Boyd said, "Most, if not all, geophysicists expect induced earthquakes to be more likely from wastewater injection rather than hydrofracking. This is because the wastewater injection tends to occur at greater depth where earthquakes are more likely to nucleate. I also agree [with Frohlich] that induced earthquakes are likely to persist for some time (months to years) after wastewater injection has ceased." Frohlich added, "Faults are everywhere. A lot of them are stuck, but if you pump water in there, it reduces friction and the fault slips a little. I can't prove that that's what happened, but it's a plausible explanation." In the US alone this correlation has been notedseveral times.
eldavojohn writes: Seven billion light years away seven billion years ago, a gamma-ray burst occurred. The observation of four Fermi-detected gamma-ray bursts (GRBs) has led physicists to speculate that space-time is indeed smooth (a prepublication PDF can be found here). Three such photons were observed to arrive very close together and the observers believe that these are from the same burst which means that there was nothing diffracting their paths from the gamma-ray burst to Earth. This observation doesn't prove that space-time is infinitesimally smooth like Einstein predicted but does give a nod that it is for a range of parameters. Before we can totally discount the theory that space-time is comprised of Planck-scale pixels, we must now establish that the proposed pixels don't disrupt the photons in ways independent of their wavelengths. For example, this observation did not disprove the possibility that the pixels exert a subtler "quadratic" influence over the photons nor could it determine the presence of birefringence — an effect that depends on the polarization of the light particles.
eldavojohn writes: Scientists have long been criticized of their inability to communicate complex ideas adequately to the rest of society. Similar to his questions on PBS' Scientific American Frontiers, actor Alan Alda wrote to the Journal of Science with a proposition called The Flame Challenge. Contestants would have to explain a flame to an eleven year old kid and the entries would be judged by thousands of children across the country. The winner of The Flame Challenge is quantum physics grad student Ben Ames whose animated video covers concepts like pyrolysis, chemiluminescence, oxidation and incandescence boiled into a humorous video complete with song. Now they are asking children age 10-12 to suggest the next question for the Flame Challenge. Kids out there, what would you like scientists to explain?
eldavojohn writes: Vermont is the first state to ban fracking (hydraulic fracturing), a process that was to revolutionize the United States' position into a major producer of natural gas. New York currently has a moratorium on fracking but it is not yet a statewide ban. Video of the signing indicates the concern over drinking water as the motivation for Vermont's measures (PDF draft of legislation). Slashdot has frequently encountered news debating the safety of such practices.
eldavojohn writes: The Logic of Chance: The Nature and Origin of Biological Evolution is a comprehensive snapshot of the latest research of biological evolution. The text is written by Eugene V. Koonin, an editor for a journal and researcher at NCBI. The book, although lacking in foundational knowledge and often foregoing explanation of research, presents a comprehensive and well-referenced view of modern evolutionary research. It is heavily laden with acronyms and jargon specific to biology and evolution. As a result, reading it requires either prior knowledge or a high tolerance for looking up these advanced topics with the reward of it being an extremely eye opening and enjoyable read worthy of your time.
First off, my background is primarily in computer science although I took courses in bioinformatics in my undergrad and have maintained an interest in evolution since evolutionary and genetic algorithms were supposed to revolutionize computer science when I was in school. Unfortunately, my lack of biology caused the text to be extremely tedious (so much googling) for some chapters while my strong statistical background made other chapters very much enjoyable. For most readers this presents a large barrier of entry. When the author discusses neural networks being used to categorize prokaryotic genes, it may be insufficient to the reader to understand what that means. As a result, this book’s audience is a relatively small set of people: 1) biology graduates with strong statistical knowledge or 2) someone willing to work very hard to understand advanced terms and concepts in both fields. Please proceed knowing that a biologist’s review of this same book could very well sound entirely different from mine. Also, Koonin wastes very few words in this book, the text is dense and if you are unable to complete reading this review due to jargon there is a low chance you’ll be able to tolerate it in the book. To sample some of this book, there is a short PDF containing chapter one or Google Books offering the first 147 pages at the time of this writing — you will see that this review barely scratches the surface of what is covered in this information-dense book.
Secondly, I will preface my review of the technical aspects of this book with my reason for giving it a score of 7 out of 10. The introduction to this book sets very lofty goals. One of them being the hope that this book does for evolution what A Brief History of Time did for physics. That is a seriously tall order and gave me correspondingly high hopes for this book. Koonin, unfortunately, is a very gifted writer and is unafraid of using exceedingly complex sentences such as this gem from page 117 (deliberately taken out of context):
"It has been known for years that a widespread form of global regulation in bacteria is mediated by cAMP, with the participation of diverse adenylate cyclases (a striking case of NOGD); numerous proteins containing cAMP sensors, such as the GAF domain; and the CRP, FNR, and other transcription regulators, also containing cAMP-binding domains."
That sentence is typical of Koonin’s writing — lengthy and intricately peppered with many acronyms (only one of which had been described well enough for me earlier in the text). Of course, that paragraph comes with a reference to a paper (like almost all of the paragraphs in this book) from 2010 by Seshasayee so the reader is free to seek external resources if these sentences are daunting.
Considering all of this, I read A Brief History of Time in high school and, despite not having had a physics course yet, learned a lot from it. I attribute that, mostly, to the fact that the sentences are simple and straightforward. Not only that but A Brief History of Time did a great job of building upward from the foundational mechanics of physics while somehow remaining refreshingly brief. This is not the case in The Logic of Chance but I will rush to the book’s defense somewhat on that charge. Prior to having read this book, I would have stated my desire that the text start from the basics and work its way up. After reading this book and understanding this field better than I ever have, I now agree that the subject matter of evolution would demand quite the epic tome to accomplish such a feat. I do hope to see future versions of this book with more concise and clear sentences as well as more fundamental concepts explained. If I could have begged Koonin to add one thing to this book, it would be a glossary in the back spanning many hundreds of pages for ignorant readers like myself. Right now this book is for graduate students and academia whereas A Brief History of Time could almost be consumed by anyone who made it through the public school system.
I also sympathize with Koonin’s herculean task because modern evolutionary studies seem relatively young compared to other fields like particle physics. As a result, Koonin must (and does) concede in some sections that there still exists largely debated theories. These debates often concern things about which we may never know the absolute truth like the branching factor of a tree of evolution on Earth some indeterminable time ago. As more and more prokaryotes and eukaryotes are added to their statistical algorithms, this may become clearer and yield revelations like the genetic makeup of the last eukaryotic common ancestor (LECA) and free this text of many pages devoted to questions surrounding such origins of life. But for now Koonin must tediously cover all his bases to introduce such things to the reader.
The book starts off by establishing the fundamentals of evolution up until the consolidation of Modern Synthesis. This includes purifying selection, drift, draft, fitness landscapes, etc until Darwinian Evolution was combined with genetics. At this point, the substrate of evolution (the genome) lead to evolutionary genomics. In particular Koonin concentrates on the statistics applied at the molecular level including distance methods, maximum parsimony, maximum likelihood, Bayesian inference and a similar analysis of phylogenetic methods. Koonin establishes early on that evolutionary research can no longer rely merely on phenotypic effects but rather there is a vast array of concrete changes happening at a molecular level.
The book moves on into comparative genomics and discusses extensively the intricate differences between the genomes of viruses, bacteria, archaea and eukaryota. Koonin exhaustively compares these groups through statistics and lays a brief foundation of relationships between genes. From this point on the book is heavily infested with the terminology of homologous, orthologous and paralogous genes. In addition to those the author discusses In-/Out-paralogous, co-orthologous and groups of orthologous (COG) genes. For people unfamiliar with this world, bookmarking and referring to Box 3-1 on page 56 is strongly advised. For the layperson, I believe an expansion of such a graphic would be a great addition to this book. Inside this part, the book also covers a simple but often misunderstood core piece of evolution and that is that evolution has the basic elementary events at the level of gene and genome evolution: substitution, deletion/loss, insertion, recombination/HGT and duplication. Over and over on Slashdot, I see comments that indicate a confusion or perception of evolution being one big monolithic thing. Koonin obviously reads or even studies a lot of other academic fields and tries to explain “the gene universe” as a space-time where there are a few dense clusters of core genes represented in most genomes but most of that space-time is occupied by a huge number of increasingly sparse “nebulae” consisting of rare genes. The author says of this universe: “This organization of the gene universe is distinctly fractal--that is, it appears at all scales of evolutionary distances.”
As if that wasn’t enough to prove that a definitive phenome narrative (what I alluded to earlier as desired) would be a bad idea, the next section moves on to systems biology and a heavier statistical look at genomics. Beyond the gene status (present or not present) exist two classes of variables: intensive evolutionary variables and extensive phenomic variables. At this point, we’re not even talking about tangible things like eye or hair color but rather the underlying mechanisms to those sorts of things like proteins and how they are folded. Everywhere Koonin uses italics, the reader should pay special attention as I found these to be the most interesting key points (example: “Highly expressed genes evolve slowly”). In defining the nature of the evolutionary process, the author covers important concepts like fitness graphs that contain multiple local maxima to demonstrate how non-optimal progressions can occur. Furthermore this section makes it clear that adaptation is not the be-all end-all of evolution. The extensive discussion of the quantifiable properties of genome architecture, functioning and evolution are defined more so by non-adaptive, stochastic processes. Here (and in many later sections) Koonin attempts to use metaphors like Jacob’s tinkering and ratchets to help the reader understand these complex concepts but I felt that these metaphors were still so far abstracted that the text could use anything linking these processes to tangible observations in organisms. Again I cannot hold this as a flaw for, after reading the book, it’s clear that such a request would be viewed as sophomoric and evidence that I am unable to progress past The Origin of the Species (this book’s key objective).
Koonin then moves on to the prokaryotic world and examines their genes and operons while paying special attention to an odd case: cyanobacteria. Most importantly in the prokaryotic domain, extensive comparative genomics has revealed a concept called horizontal gene transfer (HGT). I was personally hoping that Koonin would seize upon this novel concept and its importance in bacterial antibiotic resistance and how bacteria can evolve to dissolve novel compounds. For better or for worse, Koonin sticks to the pure purpose of this book and extensively covers important HGT discoveries like the convergence of protein sequences in similar groups of bacteria and archaea. Some selfish genes rely so heavily on horizontal mobility that they are dubbed “mobilomes” and Koonin discusses their aspects extensively. Darwin’s Tree of Life concept was a very small eukaryotic part of the big picture that Koonin tries to re-invent as the “Forest of Life” or “Web of Life” (considering HGT). A whole chapter is devoted to discussing its properties and graphically visualizing its structure based on extensive surveys and what we know today.
From there the author discusses the origins of eukaryotes, Last Eukaryotic Common Ancestor (LECA), the branching factor of its evolution, its relative distance to the point of symbiogenesis in proposed evolutionary trees and the many competing theories about that tree. This section of the book spends considerable time examining the inferred origins of basic eukaryotic cell functioning and also discusses at length the archaeal roots of elaborate systems with the exception of the mitochondrion. This chapter also looks at the perplexing features of introns in eukaryotic genes. Koonin then tackles the misconceptions and abuses of the word complexity in all aspects of evolution. He applies information theory to the genetic code and notes that “information (entropy) tells us very little about the meaningful information content or complexity of a genomic sequence.” It is then suggested that a new way to compute entropy and complexity is to examine the alignment of orthologous sequences instead of single sequences. For people interested in information theory, chapter eight is the most fruitful where Koonin proposes a computable formula for biological (evolutionary) information density. Like Claude Shannon’s ability to infer many important aspects of communication, Koonin’s modifications allow us to calculate that perceptually complex organisms possess more “entropic” genomes while perceptually less complex organisms like bacteria have the tightly packed and information dense “informational” genomes. After establishing these studies in information theory, Koonin is able to argue that neutrality of mutations that are fixed during evolution is the null hypothesis for all molecular evolutionary theories. All of this aids the author in discussing why evolution progressed passed single celled organisms that already had 1,000 to 1,500 genes to larger sets of genes in multicelled organisms.
Chapter nine tackles the modalities of Darwinian, Larmarckian and Wrightean evolutionary theories. This chapter improves upon the simplistic triad of heredity-variance-selection that defines Modern Synthesis by showing that the relationship between population size and environmental stress determines which of the three modalities is expressed the most in evolution while at the same time observing the importance of entropy (noise) at all levels of transmission. Koonin shows that by combining very well known molecular mechanisms we can achieve a complex scenario like Jean-Bapteste Lamarck’s proposed modality of evolution. The text gives viruses the same treatment which, despite my assumption that they would be easier to analyze, appear to have many of the same complexities that prokaryotes and eukaryotes have. Possibly even more so given the effects of the Red Queen Hypothesis and all of the counterdefense genomes in some viruses. Furthermore the cellular empire and virus empires have two-way exchanges of genes. The truth is we know very little about the virus world — considering its size and history — and the author postulates that viromes in unknown and unstudied viruses consist largely of uncharacterized “dark matter” (again, borrowing terms from cosmologists).
Koonin then approaches the next logical step backwards: the last universal common ancestor (LUCA). He starts by listing the arguments that cellular life indeed had a common ancestor and looks at competing theories (for example cell organization complexity versus genetic complexity leading to different models of varying degrees of cellularity). In chapter twelve, Koonin covers the topic that is often the hardest to imagine — the origin of life. This is interesting and particularly difficult because the translation system itself at some point evolved. Interestingly enough, these 60 protein-coding genes and ~40 structural RNA genes are the only complex ensemble of genes that are conserved across all extant cellular life forms. So, of course, the point in the evolutionary tree where this had developed is discussed as well as the Darwin-Eigen cycle. The latter requiring a system of a far greater complexity in order to be started. So the author begins examining the proposition that over time and due to their catalytic properties ribozymes lead to processive synthesis of peptides (long enough to be the first proteins). After discussing the eleven stages this would have to encompass, the author discusses the existing skepticism of models that try to explain how replication and transcription came about. This chapter also tackles geochemical and chemical propositions on the origin of life — something that has been discussed on Slashdot before. This research centers on networks of inorganic compartments consisting of catalytic surfaces with gradients of heat and acidity that could have supported primordial organic chemistry.
The book ends with a chapter devoted to reiterating topics as well as asking important questions like whether or not another biological evolution model is necessary/feasible as well as caution against logic like the progress fallacy or criticizing a concept like “the selfish gene” because it sounds “undignified.” Though these are tempting arguments because of their simplicity, they have proven fruitless. A diagram on page 412 reminds us just how complex the flow of genetic material is between the virus empire and the cellular empire.
There are two appendices to this book and, perhaps because they use a softer language, they were much more accessible to me yet posed more questions than answers. Appendix A concentrates on the philosophy of postmodernism, the infeasibility of synthesis and the distrust of metanarratives. The author argues that any paradigm presented must include oversimplification and that we merely replace them with better metanarratives. It is also important to ask these questions about the current paradigms for without them we would never have come up with drift, draft and various neutral ratchets to improve old models. Koonin references Hawking and Mlodinow with the concept of model-dependent realism which stresses that scientists merely construct models that are in turn swapped out for better models given how well they explain data and predict the outcomes of experiments. Lastly Koonin refers to Popper’s famous falsification paradigm and his subsequent position on how invaluable evolution is purely on the grounds that it arms us to model and understand specific experiments. The second appendix deals with roughly estimating the probability of life arising given inflationary cosmology. I know this back of the envelope math has become popular given recent discoveries of exoplanets in the news but I felt the few references to the “many worlds in one” model deserved to be placed in a separate book. Nevertheless, Koonin covers both the strong and weak forms of the anthropic principle and looks at the connotations they hold for evolution.
The references at the end of this book are extensive — 38 pages of two line references. It should probably be mentioned that Koonin’s references to his own work consist of two of these pages although at no point did it sound like he was unfairly proffering his theories over others. At certain points I had to wonder whether or not I was reading a lightly adjusted abstract from a peer reviewed paper or a book. This is most evident in one of the figures of an appendix on page 437 that reads “This is a formulation of the ‘weak’ anthropic principle adopted for the context of this paper.” Since it is a graphic and in the appendix, it’s forgivable but caused me to wonder if the rest of the book couldn’t be more seamlessly tied together with transitionary language for novices like myself. Amazingly, I found maybe one grammatical error and no typos in this book which was a refreshing experience for a first edition. Also, this is one of the best bound books I’ve had the pleasure of reading, its spine has held up to hours of laying it flat open while I googled for a better understanding. While $50 is pricey, the book is built to last and this $10 premium over the kindle edition is worth it if you must hold a physical copy of a book. It saddened me to be reminded that some states struggle with including the core concepts of Darwinian evolution anywhere in their K-12 curriculum. And should those students desire to break new ground in this modern field, texts like The Logic of Chance are that much further away from them.
eldavojohn writes: The New York Review of Books has an article penned by Steven Weinberg lamenting the future of physics, cosmology and this era of "big science" in which we find ourselves. A quote from Goldhaber sums up the problem nicely, 'The first to disintegrate a nucleus was Rutherford, and there is a picture of him holding the apparatus in his lap. I then always remember the later picture when one of the famous cyclotrons was built at Berkeley, and all of the people were sitting in the lap of the cyclotron.' The article is lengthy with a history of big physics projects (most painfully perhaps the SSC) but Weinberg's message ultimately comes across as pessimism laced with fatalism — easily understandable given his experiences with government funding. Unfortunately he notes, 'Big science has the special problem that it can’t easily be scaled down. It does no good to build an accelerator tunnel that only goes halfway around the circle.' Apparently this article mirrors his talk given in January at the American Astronomical Society. If not our government, will anyone fund these immense projects or will physics slowly grind to a halt due to fiscal constraints?
eldavojohn writes: The editors of Infection and Immunity are sending a warning signal about modern science. Two editorials (1 and 2) published in the journal have given other biomedical researchers pause to ask if modern science is dysfunctional. Readers familiar with the state of academia may not be surprised but the claims have been presented today to the National Academy of Sciences (NAS) that level the following allegations: "Incentives have evolved over the decades to encourage some behaviors that are detrimental to good science" and "The surest ticket to getting a grant or job is getting published in a high profile journal, this is an unhealthy belief that can lead a scientist to engage in sensationalism and sometimes even dishonest behavior to salvage their career." The data to back up such slanderous claims? "In the past decade the number of retraction notices for scientific journals has increased more than 10-fold while the number of journals articles published has only increased by 44%." At least a few of such retractions have been covered here.
eldavojohn writes: Using radio telescope data, scientists from around the world have plotted the Milky Way Galaxy's magnetic field in the form of Faraday Depth. From the article, 'For 150 years, scientists have measured cosmic magnetic field by observing the Faraday effect. They know that when polarized light passes though a magnetized medium, the plane of polarization turns. This concept is called Faraday rotation. The strength and direction of the magnetic field governs the amount of rotation that occurs. So scientists observe the rotation to investigate the magnetic fields' properties. Radio astronomers study the polarized light from distant radio source, passing through the Milky Way on the way to Earth, in order to measure our Galaxy's magnetic field. By measuring the polarization of the light sources at different frequencies, researchers can determine the amount of Faraday rotation.' In the future, radio telescope technologies like LOFAR, eVLA, ASKAP, MeerKAT and the SKA hope to provide enhanced Faraday rotation data so scientists can better understand turbulence in galactic gas and these galactic magnetic field structures.
eldavojohn writes: The latest proposed cause of colony collapse disorder has been published in PLOS ONE citing a 'new' parasitic fly that disorients bees who eventually die. Afterwards the larvae from the fly crawl out of the bee. It was accidentally stumbled upon by a professor collecting random dead bees as food for his mantis and leaving them alone long enough for the larva to 'hatch.' The published paper proposes this as the primary suspect as the bees seem to become disoriented and leave only to die off somewhere probably alone and not in clusters. This would explain why CCD has not resulted in bee graveyards surrounding hives. From the article, 'The parasitic fly lays eggs in a bee’s abdomen. Several days later, the parasitized bee bumbles out of the hives—often at night—on a solo mission to nowhere. These bees often fly toward light and wind up unable to control their own bodies. After a bee dies, as many as 13 fly larvae crawl out from the bee’s neck. The bees’ behavior seems similar to that of ants that are parasitized—and then decapitated from within—by other fly larvae from the Apocephalus genus.' What this means is that beekeepers can collect bees in a light trap at night and keep them in a jar to see if Apocephalus genus larvae emerge. Employ skepticism as Slashdot has reported on prior occasions that the confirmed culprit is anything from fungus to pesticide.
eldavojohn writes: The first man-made craft to do so is now entering a 'cosmic purgatory' between solar systems and entering an interstellar space of the Milky Way Galaxy. With much anticipation, Voyager 1 is now 'in a stagnation region in the outermost layer of the bubble around our solar system. Voyager is showing that what is outside is pushing back.' After three decades the spacecraft is still operating and apparently has enough power and fuel to continue to do so until 2020. The first big piece of news? "We've been using the flow of energetic charged particles at Voyager 1 as a kind of wind sock to estimate the solar wind velocity. We've found that the wind speeds are low in this region and gust erratically. For the first time, the wind even blows back at us. We are evidently traveling in completely new territory. Scientists had suggested previously that there might be a stagnation layer, but we weren't sure it existed until now." This process could take months to years to completely leave the outer shell but already scientists are receiving valuable information.
eldavojohn writes: Helium white dwarf stars are now theorized to produce a new kind of quasiparticle that would explain a known temperature anomaly between helium white dwarfs and vanilla white dwarfs (lumps of charcoal). Since helium can form a Bose-Einstein condensate and there are extra constraints inside such a dense object, a new quasiparticle emerges. Their models claim it 'reduces the specific heat of the white dwarf core by two orders of magnitude compared to a crystalline core.' But even with that figured in, measurements of some nearby ancient helium white dwarfs show that they don't fit the specific temperature curve exactly. So some questions remain with the possible explanation that these stars undergo internal transition late in their age. The heavy reading is available on the prepublication site arxiv.
eldavojohn writes: Wuhan University researchers working with the National Research Council of Canada and the Center for Functional Genomics at the University at Albany have announced that they have genetically modified rice to produce a medically useful protein chemically identical to human serum albumin. This protein is used to treat burns, traumatic shock and liver disease at a global demand rate of 500 tons each year. Normally this would be extracted from blood donations but now you can just grow rice and extract it at a rate of 2.75 grams of protein per kilogram of rice. After testing on rats with liver cirrhosis, the same response was shown as the protein from blood. This is important for China after a spike in demand and lack of supply lead to fake albumin medicine flowing through Chinese hospitals. Worried about these GMO crops cross pollinating regular crops? The researchers referred to a study indicating "a very low frequency (0.04-0.80%) of pollen-mediated gene flow between genetically modified (GM) rice and adjacent non-GM plants." Nature has a slightly more detailed article with a reference to the peer review publication.