Here is a good introduction to CRISPR/Cas9, where it came from, and how it works.
Tuesday, May 03, 2016
Here is a good introduction to CRISPR/Cas9, where it came from, and how it works.
Posted by Rob at 5:40 PM
Tuesday, February 02, 2016
Posted by Rob at 2:03 PM
Thursday, September 24, 2015
|This doctor has a tattoo that reads, "No CPR" as a living will.|
Unfortunately many of us will, one day, have to make choices about aggressive interventions aimed at prolonging our lives. The default is, of course, do everything possible since life is precious and our family and friends want to keep us around. It has been known for quite sometime however that doctors themselves are less likely to opt for aggressive interventions near the end of their natural lifespan. I first heard of this on an old radiolab podcast I listened to recently, The Bitter End.
Somewhat related is a freakonomics podcast I also recently listened to about the costs associated with end-of-life care and whether we should be given the option to take the money instead of the intervention.
I don't know what I find more disturbing: that some doctors give interventions to their patients that they would not have done to themselves, that some doctors are so traumatized by what happens frequently during end-of-life interventions, or that some of those with the most experience think that modern medicine has the wrong emphasis for end-of-life care. Maybe I'll ask for the money.
Posted by Rob at 4:36 PM
Friday, July 03, 2015
Bikes are a pretty cool intersection of physics and muscle memory. This first video is about the physics of how bikes are so stable.
This second video is about the backwards bicycle and some insights into neuroplasticity
And then, of course, bicycles and robots.
Posted by Rob at 4:30 PM
Monday, April 27, 2015
The currently inactive hardware is a pulse oximeter which, as previously mentioned, enables the noninvasive measurement of blood oxygen content. You may recognize a pulse oximeter as the red light that is clamped onto a patients finger in a hospital.
If the FDA approves the device for any medical application the implications would be interesting. The amount of health related data that could be collected would be enormous, and would likely reveal some interesting and unexpected correlations.
I'm somewhat unclear as to the range of potential applications for the individual user. The pulse oximeter seems to have applications in an acute medical setting, but I'm not clear on the usefulness in an everyday setting. It may have applications for analysis of sleeping disorders, chronic disease, or for serious athletes doing high altitude training, but otherwise I'm not sure of its utility. Could it be useful for alerting care givers to out-patient emergencies? Perhaps the use of the device will become apparent once deployed on a large scale and everyday activity data is collected.
Posted by Rob at 2:15 PM
Monday, April 13, 2015
Posted by Rob at 3:25 PM
Wednesday, April 08, 2015
Posted by Rob at 3:51 PM
Friday, February 13, 2015
|R.M.Hantemirov - Institute of Plant and Animal Ecology. Summer temperature anomalies of the Yamal Pennisula.|
Dendroclimatologists have developed methods to ensure that the samples examined contain tree ring properties that best reflect only the climactic parameter of interest. Despite this there are confounding factors, as outlined in the dendroclimatology wikipedia entry, including nonlinear responses and environmental conditions and events that can otherwise affect tree ring width and density. The most interesting confounding effect has only been evident since the 1950s and is known as the divergence problem.
The divergence problem was first identified in Alaska by Taubes (1995) and Jacoby & d'Arrigo (1995). The recognition that this problem was widespread in high northern latitudes was published in 1998 by Keith Briffa. A study by Cook in 2004 demonstrated that the problem is unique in the past 1000 years, suggesting the possibility of an anthropogenic cause. The problem is that, in northern latitudes, tree ring proxy measurements have diverged from instrument-based temperature data since the 1950s (see figure below). Growth of trees at these latitudes is declining despite instrument-based temperature data that would normally correlate with increased tree-ring width. The cause is unknown but it is likely to be a combination of local and global factors such as global warming-induced drought and global dimming.
Dendroclimatology seems like a fascinating field that, given some reasonably inexpensive equipment, could be done as an amateur. It would be a great excuse for a hike or backcountry ski while collecting data and learning about botany, local climate, local geography, statistical analysis, and sampling methods.
 Taubes, G. (17 March 1995), "Is a Warmer Climate Wilting the Forests of the North?", Science 267 (5204): 1595–1526.
 Jacoby, G. C.; d'Arrigo, R. D. (June 1995), "Tree ring width and density evidence of climatic and potential forest change in Alaska", Global Biogeochemical Cycles 9 (2): 227.
 Briffa, Keith R.; Schweingruber, F. H.; Jones, Phil D.; Osborn, Tim J.; Shiyatov, S. G.; Vaganov, E. A. (12 February 1998), "Reduced sensitivity of recent tree-growth to temperature at high northern latitudes", Nature 391 (6668): 678.
 Cook 2004
 d'Arrigo, R.; Wilson, R.; Liepert, B.; Cherubini, P. (February 2008), "On the 'Divergence Problem' in Northern Forests: A review of the tree-ring evidence and possible causes", Global and Planetary Change 60 (3–4): 289.
Posted by Rob at 5:43 PM
Wednesday, February 04, 2015
Posted by Rob at 6:55 PM
Monday, December 15, 2014
This was probably the best defence of homeopathy I have ever seen. Despite this, with his usual style, Dawkins had Dr. Fisher on the ropes the entire time without even citing the evidence for a lack of homeopathic efficacy. Admittedly Dr. Fisher is an easy target, however I would hate to have to debate Dawkins on any subject. He finds common ground, concedes valid points, asks great questions, and lets his opponent talk him/herself into tight corners. From my biased perspective, in this interview Dawkins essentially had Dr. Fisher admit that homeopathy is a form of placebo. However, is there any context in which homeopathy could provide a safe, cost-effective treatment that is completely placebo? Probably not, however water is pretty cheap and safe.
Posted by Rob at 3:33 PM
Wednesday, December 03, 2014
Here is a link to a paper on the identification of the remains of Richard III in the proprietary ReadCube format.
Posted by Rob at 2:34 PM
Monday, November 17, 2014
Posted by Rob at 3:40 PM
Monday, November 10, 2014
Posted by Rob at 7:24 PM
Friday, November 07, 2014
High altitude environments present many challenges for human physiology. These challenges are due to the thin air at higher elevations. The partial pressure of oxygen decreases with air pressure and air pressure decreases exponentially with altitude. Air pressure is half of sea-level air pressure at 5000m. This decreased availability of oxygen at higher altitudes, or hypoxia, causes altitude sickness and potentially fatal high altitude pulmonary edema and high altitude cerebral edema. The frequency of these conditions and others increase with increasing altitude.
Mere mortal lowlanders are able to partially adapt to these physiological challenges. Initially, low oxygen partial pressure is detected by the carotid body triggering increased breathing rate. Additionally at high altitudes the heart beats faster with a lower stroke volume. Longer term exposure, over days or weeks, results in further acclimatization to altitude. The most well known acclimatization feature is an increase in hemoglobin and red blood cell (RBC) mass in order to increase the amount of oxygen that can be carried by the blood. Increased RBC mass leads to increased demand on the heart, and other complications such as hypertension, chronic mountain sickness, and high fetal mortality.
The Tibetan highlanders often live at elevations of over 3500m above sea level. One of the hallmark evolutionary adaptation of these populations is a lack of increased hemoglobin at high elevations correlating with a variant of the HIF2A gene encoding HIF2alpha. The HIF2alpha transcription factor protein is active under low oxygen conditions and helps control RBC production. The HIF2A gene variant found in Tibetan highlanders traces its ancestry to a recently discovered extinct human relative - the Densisovans. So this particular adaptation is due to interbreeding between the Denisovans and the ancestors of modern Tibetans. EGLN1 and PPARA are also positively correlated with Tibetans low hemoglobin adaptation to hypoxia. Other unique traits of Tibetans contribute to their altitude aptitude including an increased basal breathing rate that does not go away when exposed to lower elevation, a larger lung capacity, and a higher blood nitric oxide (NO) concentration which can help blood vessel dilation and circulation. Tibetans also have experienced selection for genes involved in metabolism, DNA damage response, DNA repair, and genes for high infant birth weight.
Genetic adaptation to high altitude among Andean populations are distinct from the Tibetan adaptations. While HIF2A and EGLN1 both exhibit evidence of selection pressure in these populations the particular variants are not associated with decreased hemoglobin. In fact these populations demonstrate the same temporary increase in hemoglobin with increasing altitude that lowlanders experience. They do have an increased oxygen level in their hemoglobin and thus a more efficient oxygen blood carrying capacity. The Andeans do not have an increased breathing rate, however one Andean subpopulation also has increased NO blood concentrations. The Andeas are the least well adapted to high altitude as evidenced by the frequency of chronic mountain sickness. An examination of Andeans with chronic mountain sickness found that many individuals have maladapted gene variants of SENP1 and ANP32D.
The Amhara of Ethiopia are also unique in their adaptations to a low oxygen, high altitude environment. This population are immune to the dangers of high elevations over 2500m, and have been inhabiting these environments for much longer, yet they do not have either the decreased hemoglobin or high oxygen saturation of the Tibetans or Andeans respectively. However one study had identified several candidate genes for involvement in high-altitude adaptation in Ethiopia. Two of these play a role in the HIF1alpha pathway, suggesting some degree of convergent evolution.
|An O2 mask is a pretty good altitude adaptation|
Posted by Rob at 7:12 PM
Tuesday, October 14, 2014
Posted by Rob at 2:46 PM
Tuesday, August 26, 2014
Posted by Kamel at 9:12 AM
Wednesday, July 16, 2014
|Slip on a shirt, slop on sunscreen, slap on a hat and wrap on shades.|
Getting lots of UV radiation causes skin damage and ages skin. A higher mean UV index has also been associated with increased incidence of melanoma in non-Hispanic whites. A prospective study of UV exposure and cancer incidence also confirms a higher incidence of melanoma in those receiving higher UV exposure. This same study however found a decreased risk of non-Hodgkin's Lymphoma and colon cancer with increasing UV exposure. The study also found significant protection from thyroid, pancreatic and squamous cell lung cancer at intermediate UV exposure levels. Over nine years this study found that UV exposure was inversely correlated to total cancer incidence. The authors hypothesize that the protective effect is due to vitamin D production that occurs in human skin under exposure to sunlight. Is it surprising that the benefits of sun exposure aren't nearly as well known as the risks? I clearly have not done a thorough literature search however there doesn't seem to be much information on UV exposure and total cancer risk. The benefits of UV exposure are possibly less established and have an unconfirmed mechanism which may contribute to the lack of publicity. Also various authorities on skin cancer encourage acquisition of vitamin D through dietary sources.
Posted by Rob at 4:20 PM
Friday, July 04, 2014
Posted by Rob at 2:27 PM
Wednesday, May 21, 2014
A past bayblab post on the topic of human pheromones suggested that there isn't much good data on the topic. A recent TED talk on the subject is an example of a good TED talk. The speaker Tristram Wyatt talks about the background and history of pheromones and the recent discovery of a potentially genuine human pheromone that acts on babies.
Posted by Rob at 11:39 AM
Friday, January 31, 2014
Posted by Rob at 3:02 PM