I'm told that the Mark IX irony meter is still being tested. It's been almost two years and those of us with the older Mark VIII meter have to be very cautious. There are just too many IDiot posts that will fry them [Turn Off Your Irony Meters Before Reading This!!!].
Here's one, for example. It's a post on Uncommon Descent that begins with a quote from a reader and is completed by Barry Arrington [Quote of the Day]. I'm not sure if either part will be safe for the Mark IX but I know my Mark VIII can't survive.
Let's look first at the quote from a reader named "logically_speaking." You need a little background in order to understand the quote.
Recall that Intelligent Design Creationism is relatively new even though some of the basic ideas have been around for centuries. It's only been about fifteen years since they claim to have developed proof of design in nature. What that means is that before about 1995 nobody was ever convinced about design so nobody ever though about a possible designer.
Here's how logically_speaking explains it ....
logically_speaking says:
In my opinion questions such as who was the designer and who designed the designer are only important after design has been detected. In fact this is how many branches of scientific endeavor must proceed. Ask any detective at a crime scene, do they ask who was the murderer before answering the question of was any murder committed in the first place.
I wonder how that's working out? If design was only detected by Bill Dembski and Michael Behe then they've only had a few years to think about who the designer might be. I wonder what they've come up with? Who are the leading suspects?
It can't be anyone from the past since, according to logically_speaking, it would have been silly to speculate about the designer before design was detected.
Or is it possible that people believed that design was detected hundreds of years ago so they have already identified the designer using the scientific endeavor? If that's true then the modern Intelligent Design Creationism detection unit has wasted its time.
Barry Arrington clarifies ....
There are two separate questions (1) was there design and (2) who was the designer. It really is a common sense observation that the second question is logically downstream from the first. It is a corollary to that common sense observation that anyone who insists that one cannot address the upstream question until one has resolved the downstream question is either deeply confused or has an agenda unconnected with discovering the truth of the matter.
Imagine that! Some people have an agenda that's unconnected with discovering the truth!
Who knew?
Don't say I didn't warn you about turning off your irony meter.
The National Science Foundation (USA) selected this year's recipients of the National Medal of Science. President Obama made the announcement last Friday [President Obama Honors Nation’s Top Scientists and Innovators].
One of the winners is Bruce Alberts. Congratulations Bruce!
Who are these people? I pride myself on being a generalist so I think I've heard of any important discoveries in biology. I may not always agree that they are ground-breaking discoveries but at least I know about them.
I think this is the very first time that I learned of an important discovery only when the Nobel Prizes are announced.
I must be getting too old for this game. From The 2014 Nobel Prize in Physiology or Medicine ...
The Nobel Prize in Physiology or Medicine 2014 was awarded with one half to John O'Keefe and the other half jointly to May-Britt Moser and Edvard I. Moser "for their discoveries of cells that constitute a positioning system in the brain".
How do we know where we are? How can we find the way from one place to another? And how can we store this information in such a way that we can immediately find the way the next time we trace the same path? This year´s Nobel Laureates have discovered a positioning system, an “inner GPS” in the brain that makes it possible to orient ourselves in space, demonstrating a cellular basis for higher cognitive function.
In 1971, John O´Keefe discovered the first component of this positioning system. He found that a type of nerve cell in an area of the brain called the hippocampus that was always activated when a rat was at a certain place in a room. Other nerve cells were activated when the rat was at other places. O´Keefe concluded that these “place cells” formed a map of the room.
More than three decades later, in 2005, May-Britt and Edvard Moser discovered another key component of the brain’s positioning system. They identified another type of nerve cell, which they called “grid cells”, that generate a coordinate system and allow for precise positioning and pathfinding. Their subsequent research showed how place and grid cells make it possible to determine position and to navigate.
The discoveries of John O´Keefe, May-Britt Moser and Edvard Moser have solved a problem that has occupied philosophers and scientists for centuries – how does the brain create a map of the space surrounding us and how can we navigate our way through a complex environment?
Is this going to be controversial?
An accommodationist is an atheist who generally believes that religion and science are compatible but certainly believes that other atheists should go easy on those who believe in gods. Jerry Coyne doesn't like some words (e.g. bl*g, d*g)) so he invented another word for accommodationists—he calls them "faithiests." I'm going to stick with accommodationist.
Alex Chituc posts at "Nonprophet Status" on the patheos website ("Hosting the Conversation on Faith"). He defends the accommodationist position and tries to lay out their position [Our 10 Commandments of Faitheism].
Here's how he explains it ...
In most debates, especially arguments over the internet, each side brings along a list of premises, premises that originally gave rise to their conclusions and often go unaddressed. Unless a counter argument addresses any of these often unstated premises, all it accomplishes is bringing in a whole new set of premises to be addressed, and nobody gets anywhere.
Given a recent list I saw floating around twitter titled "10 commandments of faitheism," which is nothing but a list of things nobody associated with the term "faitheist" actually believes, I thought it would be a good exercise to try to list all of premises that we at NPS, at least, bring to the table. I should state upfront that, obviously, only Chris Stedman can speak for Chris Stedman, but since most people lump us at NPS in with him anyway and “faitheist” is the most convenient term on hand right now, I decided to use it.
This is a laudable objective. I fully support the concept.
Let's see how he interprets his opponents (I am one) and let's see whether his accomodationist premises stand up to close scrutiny. Here's Alex Chitic's "10 Premises of Faitheism."
There are many ideas about the origin of life but the only ones that concern me are the scientific ones. The 21st century debate mostly involves smokers vs. soupers [Changing Ideas About The Origin Of Life].
Soupers are people who believe in some version of the primordial soup. They believe that life originated in a solution of organic molecules and the most primitive way of getting energy was by oxidizing these molecules. For them, the first biochemical pathways were like glycolysis. Most of them think that complex organic molecules were delivered to Earth by asteroids [see NASA Confusion About the Origin of Life].
Smokers, on the other hand, promote an origin of life scenario that relies on the chemistry surrounding hydrothermal vents on the ocean floor. These environments favor reactions that build up organic molecules from inorganic substrates like hydrogen and carbon dioxide. In this case, the most primitive reactions are simple oxidation-reduction reactions and the most primitive pathways are biosynthesis pathways, not catabolism. This view is often referred to as "metabolism first" [Metabolism First and the Origin of Life].
A reader alerted me to a paper published last year by all the big names in metabolism first [Sousa et al., 2013]. It's an excellent paper. You should read this paper if you really want to learn about modern thinking on the origin of life problem. The biochemistry is complicated but well worth the effort.
I don't have time to explain it all. Here's a teaser ...
At first sight, the idea that chemiosmosis is a very ancient means of energy transduction might seem counterintuitive. More familiar to many is the old (and popular) doctrine that the most ancient pathway of energy metabolism is a fermentation such as glycolysis [77], an idea that goes back at least to Haldane [2] and hence arose long before anyone had a clue that biological energy can be harnessed in a manner that does not involve substrate-level phosphorylations and ‘high-energy’ bonds [149,150]. In modern life, all biological energy in the form of ATP comes ultimately from chemiosmotic coupling [151], the process of charge separation from the inside of the cell to the outside, and the harnessing of that electrochemical gradient via a coupling factor, an ATPase of the rotor–stator-type. It was not until the 1970s that it became generally apparent that Mitchell [152] was right, his Nobel prize coming in 1978, and it is hard to say when it became clear to microbiologists that all fermentative organisms are derived from chemiosmotic ancestors. We also note that Mitchell's consideration of the problem of the origin of life introduced key concepts of his later chemiosmotic hypothesis, including a definition of life as process, and the idea of vectorial catalysis across a membrane boundary that is inseparable either from the environment or from the organism itself [153].
The maxim that glycolysis is ancient might be an artefact of experience, since it was the first pathway both to be discovered and that we learned in college; in that sense, it really is the oldest. When one suggests that chemiosmotic coupling in methanogens or acetogens might be ancient, many listeners and readers shy away, mainly because the pathways are unfamiliar and often entail dreaded cofactor names.
Sousa, F.L., Thiergart, T., Landan, G., Nelson-Sathi, S., Pereira, I. A., Allen, J.F., Lane, N. and Martin, W.F. (2013) Early bioenergetic evolution. Philosophical Transactions of the Royal Society B: Biological Sciences 368:20130088. [doi: 10.1098/rstb.2013.0088]
There used to be a federal law in Germany that forbade charging tuition at German universities. The court decided in 2005 that it was okay to charge a moderate fee (€1,000). Gradually, over the next few years, 10 states introduced moderate tuition fees.
This proved so unpopular that parties supporting no tuition won elections in most of those states and next year the last state charging tuition (Lower Saxony) will stop. There will be no charge to students to attend university at every German university [Germany’s great tuition fees U-turn].
Germany is not alone. There are many European countries that provide a public university education at no charge to the student. (It's not "free"—the government pays and taxes cover the cost.)
Why can't we do this in Canada? Why can't they do it in the USA?
Another year, another "Science" Fair. The winners of the Google Science Fair 2014 have just been announced. Congratulations to all the winners.
It's time for my regular tirade about the difference between science and technology. Look at the list of projects (below). Most of these studies would be carried out in Engineering Faculties or in Clinical Departments at hospitals. Most of them are better described as engineering or technology and not science.
I think there should be two categories at most "science" fairs: one should be "science" and the other should be "engineering and technology."
What's amazing about the list is the tiny number of projects that are actually investigating the basics of how the universe works (naturalism). There's only one project on astronomy and none on geology. There's a couple that may count as chemistry. I don't see any that are looking at basic concepts in biochemistry. Most of physics isn't represented. There's hardly any mention of evolution.
I do understand why students are interested in the applications of scientific knowledge but I fear that we are not spending enough time teaching about the value of fundamental research (basic science). Is there something we can do to change this?
- Efficient management and use of rain in the Tilacancha basin, Chachapoyas, Amazonas, Peru.
- FABRICATION AND CHARACTERIZATION OF CARBON NANOTUBE DOPED ORGANIC SOLAR CELLS
- The Synthesis of Oleic Acid Core Silica Nanoparticles for the Safe Delivery of Enzymes
- Determining the ideal pendulum tuned mass damper length for optimal reduction of building earthquake resonance
- UTILISATION OF SOLAR ENERGY BY MAKING SOLAR WATER SPRINKLER
- Quantifying the Carbon Footprint of Academic Institutions to Address Systemic Inefficiencies
- Fruit Fly-Inspired Flying Robots
- "Krishak": Empowering farmers for better agriculture outcomes!
- Novel Artificial Neural Networks For 3D Chromosome Reconstruction Bias Correction
- Using Measures of Diversity and Disturbance to Assess Eelgrass Restoration Sites
- The ThereNIM: A Touchless Respiratory Monitor
- The Effect of Water Salinity on the Vitamin C in Radishes
- MASE – Selective Absorption Membrane
- Device for Associating Colors with Sounds
- Preparation of PS/PMMA Polymer Nanocomposites containing Ag Nanoparticles and their Physical Properties
- Stopping the Sahara: Building a Barrier against Desertification
- Developing Arginine as Inhibitor of alpha-synuclein aggregation- Innovative Therapy to Combat Parkinson's Disease
- Caloric Content of Zoo Animal Food
- The Effects Of Atmospheric Circulation On The Water Balance in Boulder, Colorado
- Effect of UV and Infrared light irradiated chitosan on Cu2+ and Ni2+ ions performance adsorption
- The SMART System - Stroke Management with Augmented Reality Technology
- Acidic pH determines if Cryptococcus neoformans can survive in the environment and within the host
- The great significance of small insects, or the impact of large earth bumblebees on tomato plants
- Effect of Amylase on Different Grains
- Development of TCO-less Dye Sensitized Solar cell: An approach to low cost solar cell
- DETECTION AND VISUALIZATION OF THE QUANTIZED BEHAVIOR OF RESISTANCE AND CONDUCTIVITY IN GOLD WIRE
- Ion Culture: Using Microbial Fuel Cells to Stimulate Plant Growth and Electricity with Kimchi
- Cleaning the world with sunscreen & pencils!
- Sustainable Electricity Generation and Water Purification
- Improving Power Plant Efficiency by Recovering Waste Heat
- The Olfactory Awakening
- Photo-realistic 3D rendering using Path tracing with dynamic recursion depth
- Study of children's fears.
- Converting Breath to Speech for the Disabled
- Smart Portable Interactive Whiteboard: A Novel HMI using 3D Vision, SVMs, and Kalman Filters
- A Novel Approach for the Rapid Detection of Food-Borne Pathogens Using Cell Imprinted Polymers
- Wheelchair Controlled by Eye Movements
- NOS ∞ [computer operating system)
- Wearable Sensors for Aging Society
- One Cent Test for Toxicity
- Rethink: Effectively Stopping Cyberbullying
- Can Learning Vocabulary Words Be Made More Efficient?
- Binaural Navigation for the Visually Impaired with a Smartphone
- Harvesting Energy From Human Interactions The Future of Renewable Energy
- Electricity Harvesting Footwear
- Virtual jogging - interactive network with Google Streetview
- Parking Pigeon: Application for Enhanced Localisation in Multi-Story Parking Lots
- A Method for the Mobile Study of Fracking Sites
- Predicting Alcohol Dependence Genetically
- Lowering costs for algae biofuel
- Computationally-Predicted Structure of Human DP Prostaglandin G-protein Coupled Receptor-Bound to Medications to Combat Cardiovascular Disease
- Using Machine Learning to Create an Efficient Irrigation Controller
- Ultrasonic burner
- An Intelligent Power Switching Device with an Energy-Saving Protocol
- A Real Time Map Based Approach to Emergency Management Systems
- Server to User Energy Infrastructure for Wireless Microwave Power Transmission
- Quiet Eye: A novel way to improve accuracy in badminton
- Construction of a light sensor to measure the light level in the surroundings and the section of the sky being observed in the telescope
- Dynamic Support Surface (Bed) for Effective Pressure Ulcer Prevention
- Sustainable Future for Endangered Species? Predicting the Impacts of Wilmar's Policy on Bornean Orangutan Populations
- The Correlation Between Highway Proximity and the Photosynthetic Rate of the Shinus terebinthifolius (Brazilian Pepper)
- Development of a cash-free cashier system
- Soil moisture sensor for plant watering
- KL_AS_YOL [painting asphalt roads with chlorophyll]
- An Enhanced Weather Forecast Model Based on Studies of Forecasted vs. Observed Weather
- Superconducting Levitation and Propulsion Control System
- A Modular House incorporating a MFC and a MEC to initiate efficient usage of resources
- Inzeolation! How zeolite and cellulose make a perfect combination for ecological, recyclable, multi-efficient thermal insulation?
- Predicting Cancer Drug Response Using Nuclear Norm Multi-Task Learning
- Somnolence Detection And Aiding System For Better Driving Conditions
- Effect of different organics on seed germination and growth of Indian economical seeds
- Correlation Analysis and Smartphone Terminals to Monitor and Analyze Geographic Relevance the of PM2.5
- The Accident Detection and Location System (ADLS)
- Identification of Gravitationally Lensed Quasars
- COMPLETE ORGANIC FARMING WITHOUT ANY MEDICINE OR HORMONE, WITH ONLY WASTE PROPOLIS
- A Simple Method for Simultaneous Wastewater Treatment and Chemical Recovery Using Temperature and Pressure Changes
- Kindling Cracker [an easy way to cut kindling]
- Detection of gamma hydroxybutyrate in acidic and sugary drinks
- Intellectual Device Capable of Diagnosing Cardiovascular Diseases
- Cleaning Up Oil Sands Waste
- Development of a Computer-Based Multi-Sensory System to Better Relay Pharmacotherapy Information
- Braille E-Book
- Enabling Situational Awareness: A Hat-Based Hands-Free Haptic Navigational Aid for the Visually Impaired
- The Charging Pan [harvesting heat waste from a kitchen stove]
- Natural Bacteria Combatting World Hunger {GRAND PRIZE WINNER!)
- Multidecadal Changes in Warm Season Convective Storms over the Northeastern United States
- Seeing Hands
- Frictionless Pedal Power Electromagnetic Induction Generator (for USB charging devices)
- Breaking the AGE Barrier! Inhibiting Advanced Glycation End-products to Combat Atherosclerosis, Cancer and Diabetic Disorders
- Common dandelion, as an indicator of geomedium well-being
- Analysis on the acute-toxicity of CeO2 nano particle
- Non-invasive Search for Optimal Cancer Treatment
- Two-hit Approach Blocking Alzheimer's β-amyloid Toxicity: Fibril Formation and Inhibition of newly characterized Oxygenase activity
- Vehicle for disabled people
- Novel Automated Next-Generation Multijunction Quantum Dot Solar Cell Designs Using Monte Carlo Modeling
- P.E.ACE (Portable.Evasive.AssistanCE)
- Haptic Feedback e-Reader for the Visually Impaired
- A Microbial Fuel Cell for the Eco-Friendly Processing of Acid Whey and Power Generation
- Jute-reinforced Polyester to Replace Steel Manhole Covers
- Remote controlled school presentation microscope
- Photovoltaic additive for paint and varnish
- Possibility of removing oil products from the water surface by means of magnetic fields
- A New Class of Pluripotent Stem Cell Cytotoxic Small Molecule
- Detergents in the lakes of Zainsk municipal area and their impact on the buoyancy of the aquatic birds
- Improving Raloxifene’s Affinity with ER-Beta Through Synergy with S-Equol as a Novel Chemopreventive Treatment
- Using the Soapnut, Spaindus Mukorossi, to prevent mosquito breeding
- Tomatricity - converged electricity
- Enhancing Solar Hydrogen Generation via Computer-Aided Development of Novel Metal Nanostructures
- Oil in the Soil
- BIOTECHNOLOGICAL METHOD DEVELOPMENT BASED ON AFFINITY MEMBRANE SYSTEM FOR ANTIBODY RECOGNITION
- Instant curd using Wrightia tinctoria plant latex as starter
- Technology of processing foliage, plastic bottles and waste paper into paper
- Advancing Cancer Research with an Integrated Repository and Search Engine for Gene Regulatory Networks
- Automated Lip-Reading Technique For Speech Disabilities By Converting Identified Visemes Into Direct Speech
- The effect of dormancy on poplar tree remediation of nitrates, phosphates, and fecal coliform
Paradigm shifts are happening all over the place (NOT!). If you look closely you can watch them happening because, as we all know, it's so obvious that the paradigm is shifting (NOT!). Apparently it's even more obvious if you don't have a clue what the paradigms are in the first place.
That's the situation for Mary Poplin, a Professor of education at Claremont Graduate University. She's a brand new contributor to Evolution News & Views (sic) and her first post is the text of the forward she wrote to Bill Dembski's new book [A Paradigm Shift in the Making: William Dembski's Revolutionary Breakthrough].
This is part of the standard hype on the IDiot blogs whenever a new book is about to appear. For the next few weeks we are going to be subjected to incessant, sycophantic, praise of Bill Dembski and his "revolutionary" work. Then comes the publication, the negative reviews, and the complaints that the reviewers don't understand Dembski and don't understand IDiots.
Here's the first two paragraphs of the forward. Doesn't this just make you want to pre-order the book (at 34% of the regular price) (NOT!)?
Scholars have long acknowledged that scientific revolutions, along with their paradigm shifts, happen in human history. Yet rarely do we have an opportunity to witness such a shift first hand or to have such a clear and careful explanation of one. William Dembski's painstakingly detailed explication of the shift from the material age to the information age in science and philosophy is a brilliant and rare example. As both a philosopher and a mathematician, Dembski is metaphysically and methodologically able to delineate this shift, having previously written in both areas as well as developed a statistical method for inferring intelligent causation.
This book extends his earlier work and asks the most basic and challenging question confronting the 21st century, namely, if matter can no longer serve as the fundamental substance of reality, what can? While matter was the only allowable answer of the past century to the question of what is ultimately real (matter's origin, on its own terms, remaining a mystery), Dembski demonstrates there would be no matter without information, and certainly no life. He thus shows that information is more fundamental than matter and that intelligible effectual information is in fact the primal substance.
I'd like to welcome Mary Poplin to the land of IDiots. I think she'll fit right in.
I wonder what Jeffrey Shallit thinks of the idea that information is the primal substance? He recently demonstrated that most IDiots don't understand information [Barry Arrington's Silly Misunderstanding] and that prompted a post on Uncommom Descent proving that Shallit was correct and IDiots really don't understand information [Darwinian Debating Devices: Fail Files 2014-09 – Jeffrey Shallit]. Shallit's response is here.
You know what's coming next? The IDiots are going to tell us that Dembski's new book will address all of the criticisms and we'll just have to go out and buy it ASAP. Meanwhile, nobody is allowed to criticize Dembski until they have read the book.
Oh, BTW, it should take several days to read the book and anyone who publishes a review before then must be lying.
This is getting soooooo boring.
At many (most?) universities in North America the selection of a new President is a very secret affair. Students and faculty are not consulted during the process and the candidates are not known. In fact, the process is so secret that the search committee can't even ask for outside advice about the candidates because that would reveal that they have applied for the job.
This is a very dangerous way to hire a university President because there's a great danger that the members of the search committee will, out of ignorance, choose someone that the university community doesn't respect. I've seen it happen at my own university and it happened at the University of Saskatchewan leading to the President being dismissed [The Board of Governors at the University of Saskatchewan fires President Ilene Busch-Vishniac].
Fortunately, Florida State University doesn't operate like that. The leading candidates for the job of President were vetted at an open forum with students and faculty members. One of the leading candidates was Republican State Senator, John Thrasher. One of the things that students and faculty learned was that Thrasher doesn't believe in evolution and doesn't believe that humans are responsible for climate change [A Creationist May Become Florida State University’s Next President].
As you might imagine, the students and faculty were opposed to hiring him as President. That didn't seem to matter to the Board of Governors who voted 12-1 to hire John Thrasher [A Creationist Just Became Florida State University’s New President] [Thrasher is choice for FSU, despite loud opposition].
From the Tallahassee Democrat ...
Storbeck/Pimentel, the search firm helping FSU select its next leader, conducted surveys following each candidate's campus forums last week. Thrasher received favorable ratings from only 11 percent of the responders, while 87 percent said he was not fit to be FSU's president. By comparison, the other three candidates had favorable scores between 78 and 91 percent.
The FSU Faculty Senate, which represents all 16 colleges at the university, passed a unanimous resolution Friday calling for the trustees to hire one of the three academics among the four finalists.
"We deserve a president who plays on the national stage, one who walks the walk, one who won't put off potential donors in the other party," Michael Buchler, a music professor and faculty senator, said during the public comment period. "FSU has never hired a president who didn't have experience in the classroom."
Apparently the Board of Governors don't care what the students and faculty think. What could possibly go wrong?
This is a video produced by TEDed. The "lesson" is by Alex Gendler. I don't know who he is and what his background is. What concerns me is whether this video makes a positive or a negative contribution to the public's understanding of evolution. Personally, I think it's another example of a video that does more harm than good.
What do you think?
I love it when new things are discovered, especially if they concern biochemistry. I'm always on the lookout for exciting discoveries that are going to make it into the next edition of my textbook.
That's why my eyes lit up (not!) when I saw this headline in Biology New Net: New mechanism in gene regulation revealed. Here's the teaser ...
The information encoded in our genes is translated into proteins, which ultimately mediate biological functions in an organism. Messenger RNA (mRNA) plays an important role, as it is the molecular template used for translation. Scientists from the Helmholtz Zentrum Muenchen and the Technische Universität Muenchen, in collaboration with international colleagues, have now unraveled a molecular mechanism of mRNA recognition, which is essential for understanding differential gene regulation in male and female organisms. The results are published in the renowned scientific journal Nature.
It took me a few minutes to track down the article because there weren't many hints in the press release. Turns out it still hasn't appeared in the print copy but it's available online.
Hennig, J., Militti, C., Popowicz, G.M., Wang, I., Sonntag, M., Geerlof, A., Gabel, F., Gebauer, F., and Sattler, M. (2014) Structural basis for the assembly of the Sxl–Unr translation regulatory complex. Nature published online Sept. 7, 2014 [doi:10.1038/nature13693]
The "new mechanism" is the binding of a protein to mRNA to block translation.
I suppose it depends on your definition of "new." We've been teaching undergraduates about this for over thirty years.
There's nothing in the paper about a new mechanism of gene regulation and there's no evidence in the press release that any of the authors make such a claim.
Biology News Net has become a joke. It's rare to see a paper that it hasn't mangled or a press release that it hasn't fallen for, hook line and sinker. I read it for amusement.
A recent report began with ... [Parts of genome without a known function may play a key role in the birth of new proteins]
Researchers in Biomedical Informatics at IMIM (Hospital del Mar Medical Research Institute) and at the Universitat Politècnica de Catalunya (UPC) have recently published a study in eLife showing that RNA called non-coding (lncRNA) plays an important role in the evolution of new proteins, some of which could have important cell functions yet to be discovered.
That sounds intriguing. Maybe I should read the paper even though it's in eLife.
It took a little more work than I expected, but eventually I found the paper (Ruiz-Orera et al., 2014). Here's the abstract.
Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides. We find that a large fraction of the lncRNAs expressed in cells from six different species is associated with ribosomes. The patterns of ribosome protection are consistent with the translation of short peptides. lncRNAs show similar coding potential and sequence constraints than evolutionary young protein coding sequences, indicating that they play an important role in de novo protein evolution.
The study suggests that a lot of "noncoding" RNAs are being translated. The products appear to be short polypeptides of less than 100 residues.
New protein encoding genes do arise from time to time although the number of proven examples is very small. Let's assume, for the sake of argument, that a new gene arises about once every million years in a given lineage. That would mean about five new genes in humans since they split from chimpanzees and that seems about right for an upper limit.
Now, if you make a lot of junk RNAs by randomly transcribing junk DNA, then some of them will undoubtedly make short polypeptides. There's a chance that random mutations will create a peptide that takes on a functional role of some kind. There's an even smaller chance that this function will confer a selective advantage on the individual carrying the mutation. That's one way new genes are born.
Is this a reason for carrying a huge amount of junk DNA in your genome and making thousands of lncRNAs? Is the potential to make a new gene one million years in the future sufficient explanation for the preservation of junk DNA? The answer is "no."
You don't have junk DNA because it might proven useful in the future. You have it because you can't get rid of it. You don't transcribe your junk DNA because it might be useful, you transcribe it because the general properties of RNA polymerase and transcription factors don't allow for perfect discrimination between real genes and junk DNA. Junk transcripts aren't translated because they contain potential coding regions, they are sometimes translated because they must, by chance, contain some open reading frames.
Sloppiness might, by accident, lead to new genes but that's not why things are sloppy. If having junk DNA were a clear advantage for future evolution then the genomes of all extant lineages should have lots of junk DNA and should make lots of lncRNAs.
Ruiz-Orera, J., Messeguer, X., Subirana, J.A., and Alba, M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife 2014;3:e03523 [doi: 10.7554/eLife.03523]
Many genes encode proteins and many other genes specify functional RNAs that do not encode proteins. The "RNA genes" include the classic genes for ribosomal RNAs and tRNAs as well as genes for very well-studied RNAs that carry out catalytic roles in the cell. There are a myriad of small RNAs required for things like splicing and regulation. All species, both prokaryotes and eukaryotes, contain genes for a wide variety or functional RNAs.
Eukaryotes seem to have an abundance of genes for small RNAs that perform a number of specific roles in regulation etc. They also have a lot of DNA regions complementary to long noncoding RNAs or lncRNAs (also lincRNA). The definition of long noncoding RNAs seems arbitrary and ambiguous [see Long Noncoding RNA]. Some of them might even encode proteins!
As a general rule, these RNAs are longer than 200 bp and some scientists put the cutoff at 1000 bp. Simple eukaryotes, such as yeast, don't have a lot of lncRNAs but eukaryotes with large complex genomes that are full of junk DNA seem to have a lot of different lncRNAs. The DNA regions1 that specify these lncRNAs ar not conserved. This strongly suggest that many of the lncRNAs are spurious nonfunctional transcripts even though some of them have well-characteized functions [see On the function of lincRNAs].
As usual, we have a definition problem. Are "lncRNAs" just a generic class of long noncoding RNAs that include thousands of nonfunctional molecules that are nothing more than junk RNA? Or, does the term "lncRNA" refer only to the subset that has a function? If it's the latter, then we should probably be referring to "putative" lncRNAs most of the time since the vast majority have not been shown to have a function. (There are about 10,000 of these RNAs in humans.)
I don't see how you can avoid the elephant in the room whenever you talk about lncRNAs. The most important question in NOT whether some of them have a function—that was demonstrated 30 years ago. The important question is whether the majority, or even a substantial minority, have a function.
That's why I was eager to read a short review by Rinn and Guttman in a recent issue of Science (Rinn and Guttman, 2014). They describe two lncRNAs that probably play a role in organizing chromatin within the nucleus (Xist and Neat1, both fram mammals). That's cool.
Then they say,
Collectively, these studies suggest that lncRNAs may shape nuclear organization by using the spatial proximity of their transcription locus as a means to target preexisting local neighborhoods. lncRNAs can in turn modify and reshape the organization of these local neighborhoods to establish new nuclear domains by interacting with various protein complexes, including chromatin regulators. Once established, a lncRNA can act to maintain these nuclear domains through active transcription and recruitment of interacting proteins to these domains. While the mechanism for how lncRNAs establish these domains is not fully understood, it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization.
It sure sounds like they are describing a particular function (nuclear organization) to the majority of lncRNAs. But what if 90% of all 10,000 lncRNAs have no function and what if only 100 of the remaining functional lncRNAs are involved in nuclear organization? That means there are 900 functional lncRNAs that play a different role in the cell?
If that were true, you would write that last paragraph very differently. If you recognize the elephant, you might say something like this ....
Very few lncRNAs have been shown to have a function and there's a very good chance that most of them are spurious transcripts that have no function. However, a small percentage do seem to have a function. In this review we have identified some long noncoding RNAs that appear to be involved in nuclear organization. We propose to call these RNAs "noRNAs" for "nuclear organizer RNAs" on the grounds that once a function has been identified we should stop referring to them as lncRNAs.
But that doesn't sound nearly as exciting as the subtitle of the article, "Long noncoding RNAs may function as organizing factors that shape the cell nucleus" or the quotation that's prominently displayed in a box in the center of the page, "... it is becoming increasingly clear that IncRNAs are important in all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization." When did science become so dedicated to hype over substance? I must have missed the memo.
1. I use "DNA regions" instead of "genes" because the definition of a gene requires that the gene product be functional. You can't call them genes unless you have demonstrated that the RNA has a function.
Rinn, J. and Guttman, M. (2014) RNA and dynamic nuclear organization. Science 345"1240-1241 [doi: 10.1126/science.1252966]
The students in my third year lab course are about to test various food products to see if they contain any DNA from genetically modified organisms. They'll be using a variety of PCR primers to detect the Cauliflower mosaic virus 35S promoter and the nopaline synthase terminator sequence from the Ti plasmid of Agrobacterium tumefaciens [see Roundup Ready® Transgenic Plants ].
Every student has to bring in their own food sample to test but I'll be providing a number of "controls" that I picked up in the cafeteria and at the grocery store. Which ones are Frankenfood?
We're using some additional sets of primers as controls. One set detects a chloroplast gene (rbcL). We have two sets of primers for corn-specific genes (invertase and zein) and one set for a soybean specific gene (lectin). An important part of the exercise is figuring out what controls to use and what DNA samples to analyze. Each group of two students can do 24 PCR reactions. It's going to be a challenge for them to figure out which reactions are the most important.
(They were told that corn and soy products are most likely to test positive in the GMO assay.)
