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Thursday, September 25, 2014

Are "science" fairs really about science?

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?
  1. Efficient management and use of rain in the Tilacancha basin, Chachapoyas, Amazonas, Peru.
  3. The Synthesis of Oleic Acid Core Silica Nanoparticles for the Safe Delivery of Enzymes
  4. Determining the ideal pendulum tuned mass damper length for optimal reduction of building earthquake resonance
  6. Quantifying the Carbon Footprint of Academic Institutions to Address Systemic Inefficiencies
  7. Fruit Fly-Inspired Flying Robots
  8. "Krishak": Empowering farmers for better agriculture outcomes!
  9. Novel Artificial Neural Networks For 3D Chromosome Reconstruction Bias Correction
  10. Using Measures of Diversity and Disturbance to Assess Eelgrass Restoration Sites
  11. The ThereNIM: A Touchless Respiratory Monitor
  12. The Effect of Water Salinity on the Vitamin C in Radishes
  13. MASE – Selective Absorption Membrane
  14. Device for Associating Colors with Sounds
  15. Preparation of PS/PMMA Polymer Nanocomposites containing Ag Nanoparticles and their Physical Properties
  16. Stopping the Sahara: Building a Barrier against Desertification
  17. Developing Arginine as Inhibitor of alpha-synuclein aggregation- Innovative Therapy to Combat Parkinson's Disease
  18. Caloric Content of Zoo Animal Food
  19. The Effects Of Atmospheric Circulation On The Water Balance in Boulder, Colorado
  20. Effect of UV and Infrared light irradiated chitosan on Cu2+ and Ni2+ ions performance adsorption
  21. The SMART System - Stroke Management with Augmented Reality Technology
  22. Acidic pH determines if Cryptococcus neoformans can survive in the environment and within the host
  23. The great significance of small insects, or the impact of large earth bumblebees on tomato plants
  24. Effect of Amylase on Different Grains
  25. Development of TCO-less Dye Sensitized Solar cell: An approach to low cost solar cell
  27. Ion Culture: Using Microbial Fuel Cells to Stimulate Plant Growth and Electricity with Kimchi
  28. Cleaning the world with sunscreen & pencils!
  29. Sustainable Electricity Generation and Water Purification
  30. Improving Power Plant Efficiency by Recovering Waste Heat
  31. The Olfactory Awakening
  32. Photo-realistic 3D rendering using Path tracing with dynamic recursion depth
  33. Study of children's fears.
  34. Converting Breath to Speech for the Disabled
  35. Smart Portable Interactive Whiteboard: A Novel HMI using 3D Vision, SVMs, and Kalman Filters
  36. A Novel Approach for the Rapid Detection of Food-Borne Pathogens Using Cell Imprinted Polymers
  37. Wheelchair Controlled by Eye Movements
  38. NOS ∞ [computer operating system)
  39. Wearable Sensors for Aging Society
  40. One Cent Test for Toxicity
  41. Rethink: Effectively Stopping Cyberbullying
  42. Can Learning Vocabulary Words Be Made More Efficient?
  43. Binaural Navigation for the Visually Impaired with a Smartphone
  44. Harvesting Energy From Human Interactions The Future of Renewable Energy
  45. Electricity Harvesting Footwear
  46. Virtual jogging - interactive network with Google Streetview
  47. Parking Pigeon: Application for Enhanced Localisation in Multi-Story Parking Lots
  48. A Method for the Mobile Study of Fracking Sites
  49. Predicting Alcohol Dependence Genetically
  50. Lowering costs for algae biofuel
  51. Computationally-Predicted Structure of Human DP Prostaglandin G-protein Coupled Receptor-Bound to Medications to Combat Cardiovascular Disease
  52. Using Machine Learning to Create an Efficient Irrigation Controller
  53. Ultrasonic burner
  54. An Intelligent Power Switching Device with an Energy-Saving Protocol
  55. A Real Time Map Based Approach to Emergency Management Systems
  56. Server to User Energy Infrastructure for Wireless Microwave Power Transmission
  57. Quiet Eye: A novel way to improve accuracy in badminton
  58. Construction of a light sensor to measure the light level in the surroundings and the section of the sky being observed in the telescope
  59. Dynamic Support Surface (Bed) for Effective Pressure Ulcer Prevention
  60. Sustainable Future for Endangered Species? Predicting the Impacts of Wilmar's Policy on Bornean Orangutan Populations
  61. The Correlation Between Highway Proximity and the Photosynthetic Rate of the Shinus terebinthifolius (Brazilian Pepper)
  62. Development of a cash-free cashier system
  63. Soil moisture sensor for plant watering
  64. KL_AS_YOL [painting asphalt roads with chlorophyll]
  65. An Enhanced Weather Forecast Model Based on Studies of Forecasted vs. Observed Weather
  66. Superconducting Levitation and Propulsion Control System
  67. A Modular House incorporating a MFC and a MEC to initiate efficient usage of resources
  68. Inzeolation! How zeolite and cellulose make a perfect combination for ecological, recyclable, multi-efficient thermal insulation?
  69. Predicting Cancer Drug Response Using Nuclear Norm Multi-Task Learning
  70. Somnolence Detection And Aiding System For Better Driving Conditions
  71. Effect of different organics on seed germination and growth of Indian economical seeds
  72. Correlation Analysis and Smartphone Terminals to Monitor and Analyze Geographic Relevance the of PM2.5
  73. The Accident Detection and Location System (ADLS)
  74. Identification of Gravitationally Lensed Quasars
  76. A Simple Method for Simultaneous Wastewater Treatment and Chemical Recovery Using Temperature and Pressure Changes
  77. Kindling Cracker [an easy way to cut kindling]
  78. Detection of gamma hydroxybutyrate in acidic and sugary drinks
  79. Intellectual Device Capable of Diagnosing Cardiovascular Diseases
  80. Cleaning Up Oil Sands Waste
  81. Development of a Computer-Based Multi-Sensory System to Better Relay Pharmacotherapy Information
  82. Braille E-Book
  83. Enabling Situational Awareness: A Hat-Based Hands-Free Haptic Navigational Aid for the Visually Impaired
  84. The Charging Pan [harvesting heat waste from a kitchen stove]
  85. Natural Bacteria Combatting World Hunger {GRAND PRIZE WINNER!)
  86. Multidecadal Changes in Warm Season Convective Storms over the Northeastern United States
  87. Seeing Hands
  88. Frictionless Pedal Power Electromagnetic Induction Generator (for USB charging devices)
  89. Breaking the AGE Barrier! Inhibiting Advanced Glycation End-products to Combat Atherosclerosis, Cancer and Diabetic Disorders
  90. Common dandelion, as an indicator of geomedium well-being
  91. Analysis on the acute-toxicity of CeO2 nano particle
  92. Non-invasive Search for Optimal Cancer Treatment
  93. Two-hit Approach Blocking Alzheimer's β-amyloid Toxicity: Fibril Formation and Inhibition of newly characterized Oxygenase activity
  94. Vehicle for disabled people
  95. Novel Automated Next-Generation Multijunction Quantum Dot Solar Cell Designs Using Monte Carlo Modeling
  96. P.E.ACE (Portable.Evasive.AssistanCE)
  97. Haptic Feedback e-Reader for the Visually Impaired
  98. A Microbial Fuel Cell for the Eco-Friendly Processing of Acid Whey and Power Generation
  99. Jute-reinforced Polyester to Replace Steel Manhole Covers
  100. Remote controlled school presentation microscope
  101. Photovoltaic additive for paint and varnish
  102. Possibility of removing oil products from the water surface by means of magnetic fields
  103. A New Class of Pluripotent Stem Cell Cytotoxic Small Molecule
  104. Detergents in the lakes of Zainsk municipal area and their impact on the buoyancy of the aquatic birds
  105. Improving Raloxifene’s Affinity with ER-Beta Through Synergy with S-Equol as a Novel Chemopreventive Treatment
  106. Using the Soapnut, Spaindus Mukorossi, to prevent mosquito breeding
  107. Tomatricity - converged electricity
  108. Enhancing Solar Hydrogen Generation via Computer-Aided Development of Novel Metal Nanostructures
  109. Oil in the Soil
  111. Instant curd using Wrightia tinctoria plant latex as starter
  112. Technology of processing foliage, plastic bottles and waste paper into paper
  113. Advancing Cancer Research with an Integrated Repository and Search Engine for Gene Regulatory Networks
  114. Automated Lip-Reading Technique For Speech Disabilities By Converting Identified Visemes Into Direct Speech
  115. The effect of dormancy on poplar tree remediation of nitrates, phosphates, and fecal coliform

A paradigm shift in the making

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.

On choosing a new university president

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?

Myths and misconceptions about evolution???

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?

Tuesday, September 23, 2014

A new mechanism of gene regulation!

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.

Monday, September 22, 2014

Are lncRNAs really mRNAs in waiting?

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]

What are lncRNAs?

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]

Monday, September 15, 2014

Looking for Frankenfood

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.)

Friday, September 12, 2014

The logic of lawyers

Barry Arrington is a lawyer from Colorado [Encyclopedia of American Loons]. Here's an example of the logic of lawyers posted on Uncommon Descent [Not Merely False].
The following statements are so obvious as to be considered truisms.

1. The primordial datum: I am subjectively self-aware.

2. It is not possible even in principle to account for mental facts, such as the primordial datum, on the basis of physical facts. They are different sorts of things; therefore one cannot account for the other. Trying to account for subjective self-awareness by suggesting it is an epiphenomenon of the electro-chemical process of the brain is like saying the color blue can be reduced to its constituent banana peels.

3. It follows that a reductionist materialism is not merely false but obviously false.

4. Just as obviously, it does not follow that committed materialists will admit that reductionist materialism is false, for they have reasons to put their faith in their metaphysical commitments that have nothing to do with the evidence and logic of the matter.
I would not want him to defend me if I were innocent. On the other hand, he might be a good choice if I were guilty because I could easily fool him into thinking that I was innocent.

Thursday, September 11, 2014

The mystery of Maud Menten

Maud Menten is best known for the Michaelis-Menten equation and her work on enzyme kinetics. She was born in Port Lambton, Ontario and she is a graduate of the University of Toronto.

The "mystery" concerns her degrees and the year she graduated. The video below was prepared when she was inducted into the Canadian Medical Hall of Fame in 1998 [Maud Menten]. If you watch the first few minutes you'll hear that in 1911 Maud Menten was one of the first Canadian women to receive a medical degree. You find similar statements all over the web, although sometimes it says she graduated in 1913—as in the text on the Canadian Hall of Fame website.

Wednesday, September 10, 2014

The perils of genetic testing

Most people don't understand the consequences of genetic testing. You may think that you can handle all of the data and information but think again.

This is the story of someone who got their DNA tested by a commercial company and he persuaded his parents to participate as well. What could possibly go wrong? The title of the article tells the story: With genetic testing, I gave my parents the gift of divorce.

Turns out he has a half-brother! His father never mentioned that he had a son with another woman.
At first, I was thinking this is the coolest genetics story, my own personal genetics story. I wasn't particularly upset about it initially, until the rest of the family found out. Their reaction was different. Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We're not anywhere close to being healed yet and I don't know how long it will take to put the pieces back together.
It's not always true that having information is better than not having information. If you beleive that then you are very naive.

The Non-Conference Is Coming

Website Countdown Clock

Do IDiots understand evolutionary theory?

Do Intelligent Design Creationists (IDiots) understand evolution? ... of course not.

It's been really frustrating over the past 25 years trying to explain modern evolutionary theory to IDiots. They continue to refer to "Darwinism" and "neo-Darwinism" but it's obvious that they don't have a clue what they mean by those terms. This become especially obvious when they discover, once again, that real evolutionary biologists don't accept the IDiots' version of evolutionary theory.

Check out the latest post by Casey Luskin on Evolution News & Views. It would be so easy for him to explain to his readers what the textbooks say on evolutionary theory and how it differs from what the IDiots are promoting in their own books and on their websites [Are Biologists Rejecting Neo-Darwinian Evolution?]. He doesn't do this, of course, and that's only partly because it suits his purpose to be dissembling. It's mostly because he really doesn't understand what he's talking about. We know this because dozens of people have tried to explain it to him over the years and he still doesn't get it.

In fairness, Casey Luskin is responding to an article on The BioLogos Forum by philosopher Robert C. Bishop [Two Rhetorical Strategies (Reviewing “Darwin’s Doubt”: Robert Bishop, Part 2)]. It's pretty clear that Bishop doesn't understand modern evolutionary theory either. Unfortunately, there are many scientists who share these misconceptions but that's not an excuse for Luskin and his fellow travelers since they are supposed to understand what they spend so much time attacking.

The atheist barmaid's error

I'm usually a big fan of Jesus and Mo but today's cartoon is a bit disappointing. It is "resurrected" from 2009 [nerve2] and it is prompted by an excellent article on militant atheists written by Nick Cohen [The phantom menace of militant atheism]. Even Jerry Coyne likes it [A wonderful attack on the "militant fundamentalist atheism" trope].

The issue here is whether an atheist needs to study all religions in order to be an atheist. The barmaid seems to concede that point since she advances arguments that require knowledge of specific religions. Both of her examples require the provisional acceptance of gods because they refer to particular properties of those gods (i.e. whether they can have sons and prophets).

A Christian, for example, would happily engage the barmaid in a debate about the the divinity of Jesus as long as they begin with the assumption that gods exist. In order to engage seriously in that debate, the barmaid would have to read a ton of Christian apologetic literature. In other words, she would have to understand "sophisticated" religion. She would not be defending atheism even if she won the debate since there are billions of religious people who don't believe in the divinity of Jesus.

But atheists, by definition, don't believe in gods. The only arguments that are relevant are whether gods exist. Those arguments are not specific to any particular religion and they certainly aren't going to be found in the Bible or the Qur'an. I do not accept the premise that gods exist so I'm not the least bit interested in studying the religious beliefs of anyone who begins with the "fact" that gods exist. I'm about as interested in debating whether any of the gods had children as I am in debating how many angels can dance on the head of a pin.1

The atheist barmaid made a mistake. She should have said "Let's see - I understand that all religions begin with the idea that gods exist. What evidence do you have that this is true?"

Or, for that matter, the problem of evil. If there are no gods then there's no problem. Debating the "problem" of evil or whether Jesus is the son of gods is just like debating the cut of the Emperor's new clothes [On the Existence of God and the Courtier's Reply].

Wednesday, September 03, 2014

Club Day at the University of Toronto

Today's the day that clubs strut their stuff and try to get new students to sign up. It's an important part of campus life and an important part of a university education even though the majority of students don't participate.

There's a club for just about everyone, even biochemists!

All of that will disappear when universities shut down and undergraduate education is confined to MOOCs and glorified Skype conferences. You can't join a rowing club if you're a thousand kilometers from the clubhouse.

I suppose there are lot of business types out there who don't care about this sort of thing as long as you pay your money, get a degree, and go on to a decent job where you can pay back your student loan.

Harrison Ford vs Ian McKellen

It's hilarious even when you know it's photoshopped.

Are universities doomed?

This month's issue of The Atlantic has another one of those boring articles on the imminent death of universities (colleges) [The Future of College?].

This time it's a new "university" called MINERVA that's going to kill off all the old-school schools. Minerva is a for-profit university where all the learning takes place in electronic seminars of up to 19 students. Sort of like a Skype conference call only it uses copyrighted software. Students will pay only $28,000 (US) per year for this experience.

There have been articles about the death of universities published every year for as long as I can remember. Almost all of them think that a "university" is just a place where you go to get an undergraduate education. That's because almost all of the potential murderers only experienced university as an undergraduate.

Tuesday, September 02, 2014

What are they playing?

Apparently the Queen's Guards surprised everyone by playing a new song during the changing of the guard at Buckingham Palace on July 15, 2014.

Name that song!

Do you know it?

Here's a hint ... the actual theme is better but it's the thought that counts.

The top ten cities in the world

The Economist has surveyed cities from all over the world to find the ones that are the most livable (i.e. best places to live). Here's a summary of the criteria described in the report [A Summary of the Liveability Ranking and Overview]
The concept of liveability is simple: it assesses which locations around the world provide the best or the worst living conditions. Assessing liveability has a broad range of uses, from benchmarking perceptions of development levels to assigning hardship allowance as part of expatriate relocation packages. The Economist Intelligence Unit’s liveability rating quantifies the challenges that might be presented to an individual’s lifestyle in any given location, and allows for direct comparison between locations.
Bjørn Østman alerted me to the list by posting a link to this article: The World's Most Livable Cities All Have One Big Thing in Common. What do the top ten cities all have in common?—none of them are in the USA.

Here's the list ....

1. Melbourne, Australia
2. Vienna, Austria
3. Vancouver, Canada
4. Toronto, Canada
5 (tie). Adelaide, Australia
5 (tie). Calgary, Canada
7. Sydney, Australia
8. Helsinki, Finland
9. Perth, Australia
10. Auckland, New Zealand

There's obviously more to "livability" than meets the eye. Some of these places are a lot less interesting than Paris, London, or New York.

I think the ranking also depends very much on how much money you have. I'd need to be offered a hell of a lot more money if I were to consider a move to Calgary, Helsinki, or Perth.1

1. I've never been to Perth but it doesn't seem like a place I'd like to live.

IDiots exploring evolution

Modern evolutionary theory is far more advanced than the simple version that's attacked by Intelligent Design Creationists. Neutral Theory, population genetics, and the importance of random genetic drift are just a few of the additions that were incorporated in the 1960s. (That's almost 50 years ago.)

Most IDiots are half-a-century behind in their knowledge of science. They think that random mutations and natural selection are the only way that evolution can occur.1 That's why they refer to evolution as "Darwinism."

Many of them have heard vague rumors of change, proving that from time to time they do, indeed, take their fingers out of their ears. They've discovered that modern scientists have moved well beyond natural selection as an explanation for every bit of evolution. This makes the IDiots very happy since, to them, it means that evolution is wrong. And if evolution is wrong then gods must exist.

They've even developed a course to explain why Neutral Theory and random genetic drift support the idea that gods must be making bacterial flagella and protein-protein contacts. It looks like a very interesting course ...

1. A few of them might know differently but they will never admit it in public.