Normally my dog’s paw pads are dark, i.e. dirty. They’re not dirty in the sense that she marks the floor everywhere she walks. We just can’t scrub her paws every time we take her out. So after her swim, I figured it would be a good chance to take a photo so you can see what is Merle in dog paw pads.
Merle is a coat pattern in dogs, not a color of coat. It can affect their paw pad color, as shown in my dog below. Merle is not to be confused with heterochromia, which is specific to the eyes. http://goo.gl/K4Djj
Merle is actually a heterozygote of an incompletely dominant gene. If two such dogs are mated, on the average one quarter of the puppies will be “double merles”. A phantom merle is one with such small patches of merle—or none at all—that it appears to be a non-merle. In America, a dog with the phantom merle coloring is described as being “cryptic for merle.”
About week ago I posted some pictures of my Hydrangeas that were just starting to bloom. http://goo.gl/Gn47h I noticed that on the same plant, some of the flowers were blue and others were pink. I knew that pH played a role but I found out that it is actually the aluminum in the soil that make the blue pigment possible. So for ScienceSunday curated by Allison Sekuler Rajini Rao Robby Bowles and me, I had to dig up more info to post along with pictures from today.
When the pH is acidic, aluminum in the soil, mostly from clay, allows a metal complex of aluminum and a anthocyanin, named delphinidin 3-monoglucoside, to form. After the pictures, the first figure is of the aluminum complex. The next figure shows various blue flowers with sections cut revealing the pigment cells and protoplasts.
Although the next two figures are about Morning glories, they were too interesting to pass up. A certain ScienceSunday co-curator always has her eyes on certain channels. Similar to the previous figure, there is a cross section-cut revealing the pigmented cells. However, the paper and figure go on to discuss how the Morning glory does not have metal complexation. The petal color changes during flower opening due to pH changes which were measured in the second part of the figure. The final figure show the purported ion channel mechanism.
Plants can be beautiful. When you throw in a dash of science, they can be beautiful and intriguing.
Edit I forgot to add that a lot of insects leave hydrangeas alone. Why? Aluminum toxicity – win – win for us gardeners.
By examining the skulls of primates and connecting the structure and function of bones Dr. Ross et al hopes to better understand the evolutionary forces that drive variations in the skulls of primates. Dr. Ross brought primate skulls on loan from the Field Museum of Natural History to the lab and I imaged them with our microCT (x-ray computed tomography) which I’ve discussed in previous #ScienceSunday posts. The theme for today’s ScienceSunday is collaborative research. So I collaborated with Erin Kane to present my collaboration with Dr. Ross. Just as in real life, working together, we can get more done and complement each other. Thanks to Erin for the beautiful write up below.
Primate Eyes
One of the defining features of all primates is our binocular vision. As primates’ ancestors took to the trees, being able to accurately judge distances gave individuals a selective advantage – you survived jumps and were able to have more offspring than individuals without depth perception who broke bones or fell out of trees. The development of binocular vision may also have helped early primates hunt insects better.
The evolution of binocular vision involved moving eyes from the side of the head (like a horse) to the front of our face, where they are today. When primates’ eyes moved to the front of their faces, this changed the distribution of forces exerted on the skull, especially when chewing. Over time, primate ancestors developed a bony ridge, called a post-orbital bar, behind their eye that kept the forces of chewing from deforming the skull and squishing the eyeball.
Tupaia is a tree shrew, one of primates’ closest relatives. Their eyes are on the sides of their faces, so their post-orbital bar isn’t complete. Cheirogaleus, the fat-tailed dwarf lemur, is a prosimian, a relatively primitive modern primate (http://goo.gl/ti65p). It’s skull is very similarly shaped to Tupaia, but it has a complete post-orbital bar, and it’s eyes are closer to the front of its face. Tuapaia is a lot like the proto-primates, organisms called plesiadapids who are likely primates’ ancestors. Cheirogaleus is a pretty good analogy for some of the early primates – nocturnal, probably eating insects, and living solitarily.
About the same time monkeys evolved, primates’ eyes shifted to the front of their faces. In response to the shift in forces from the eyes moving further to the front of their faces, monkeys and apes developed a solid plate of bone at the back of their eyes. Saguinus and Aotus are both South American monkeys with that solid plate of bone at the back of their eyes. Sagiunus is a diurnal monkey, active during the day. Its eyes are much smaller than Aotus, the only nocturnal monkey. Nocturnal primates have really large eyes (compare Aotus and Cheirogaleus) in order to get as much light as possible into their eyes.
Enjoy your collaborations, Memorial Day in the US, and The Monkees.
Here’s a news article, In cancer science, many ‘discoveries’ don’t hold up, about an oncology researcher trying to replicate some preclinical studies before moving forward with potential drug development. (thanks to a post via Branimir Vasilić http://goo.gl/wJyMx)
The news article summarizes a commentary in the journal Nature, titled, Drug development: Raise standards for preclinical cancer research.
Notice the difference in the titles? Here’s a similar discussion where Rajini Rao points out that the news article is titled, Eggs unlimited: an extraordinary tale of scientific discovery vs. Potential Egg Stem Cells Reignite Debate in the journal Science. Similar discussion here: http://goo.gl/Yq1ls
I want to focus on the oncology debate since I do cancer research. However, the comments from the article and me are relevant to many areas of research.
Drug development: Raise standards for preclinical cancer research
C. Glenn Begley & Lee M. Ellis
Nature 483, 531–533 (29 March 2012) doi:10.1038/483531a
Published online 28 March 2012
Here are 5 reasons why oncology research might not be replicated
Endpoints
As the authors point out, endpoints in cancer research can be less quantitative compared to say statin research where cholesterol level is the endpoint. In cancer studies sometimes tumor size is an endpoint. As an imaging person, my field very frequently frowns on this, as a drug can cause tumor swelling, i.e., increase in size, while actually causing tumor cell death. Not everyone has access to expensive imaging equipment or the skills to utilize many imaging modalities. So a lot of cancer drug researchers rely on caliper measurements of the tumor even though most would acknowledge that a tumor is rarely a perfect sphere where one only needs to measure the diameter.
Cutting edge
The authors suggest that some of the irreproducible results could be due to publications that were cutting edge, i.e., a researcher found something completely new or unexpected and published quickly. Also some technology might not be available to Amgen that was used in one of the publications. For example oxygen imaging is available in maybe 3-4 labs in the world.
Competition
Although this may sound terrible to the general public, there have been cases where researchers have omitted a key ingredient or step on a method in order to keep a competitive advantage.
Narrow scope
Begley and Ellis state that the robustness of some results were checked. For example, a publication might get phenomenal results with a particular tumor cell-line or model. When Amgen tried to broaden the scope, e.g., trying a different cell-line or model, the “narrow” promising results turned out to be less robust.
Statistics
Another issue is improper statistics. Quite often scientist haven’t had enough statistical training or do not consult a statistician and therefore use an incorrect method or interpretation.
Conclusion
Interestingly, Begley mentions that the results do not use enough predictive biomarkers (an area of focus for my research which I hope to contribute a solution). The authors’ suggestion to try to show tumor models where there is a negative result is often not possible when a grant funds a particular cancer or model. I totally agree about the selective presentation aspect of their paper. Unfortunately, I don’t think it is uncommon for a publication to have a figure that is stated to be “representative” of all the data, when in fact it was carefully selected as the best example. As some commenters on the online version of this Nature article state, it’s interesting that Begley and Ellis do not list the publications they tried to replicate, thereby limiting the possibility to replicated their article. Transparency?
Edit: I want to be clear that I don’t condone some of these reasons for the lack of reproducible publications. I want to emphasize that there are some reasons why a drug company might not be able to replicate a publication and therefore, there is no need for Reuters or Yahoo news to say the sky is falling for scientist.
