I had not heard of Crystallofolia before Michael O’Reilly’s post. It’s beautiful and interesting.
From Latin crystallus ice [itself from Greek κρυσταλλος; cf. κρυος ‘frost’]and folium leaf. These elegant formations have been given many names, metaphorical in nature, most commonly ‘frost flowers’ (or ribbons), a formation which is neither frost nor a flower. These common names, however, are easily confused with terms describing true frost from condensation on a cold surface as well as any picturesque ice formation. These frost metaphors are of fairly recent origin, not current with 19th Century treatments of the subject (e.g., ‘frost freak’ was used by several scholars). I thus propose folium, leaf, as a more appropriate metaphor, since like leaves these formations emerge laterally from the stem, and the enormous diversity of forms finds better matches with leaves than with flowers and ribbons — although this is perhaps less poetic. Perhaps more significantly, the physical process by which water moves to the ice formations is analogous to the transpiration that brings water from the roots to the leaves. My perspective is not new: German botanists in the 19th Century used the term ‘Eisblatt’ (‘ice leaf’).
Read the source below for more information about this phenomenon.
Last night we had our first hard freeze of the year, and the frostweed in our yard put on a little performance. Basically the water inside the frostweed freezes and extrudes from splits in the stem in fascinating ribbons and whorls. Here’s a shot of one of the splits with the ice curling around the stem. The ribbons are unbelievably thin, and it makes a pretty effect. A couple of the sections were over a foot tall, with the ice going in several directions.
Maclura pomifera is a tree that grows throughout the US and part of southeastern Canada. It’s related to the mulberry tree although the fruit would make you think it’s citrus. The Osage Indians used it’s wood to make bows and clubs due to it’s resistance to decay and durability. It’s no surprise that modern use of the wood is for fence posts and tool handles. The tree was planted in rows in the Great Plains states to help break the wind, hence the nickname “hedge apple”. The fruit used to be placed under the bed to repel some insects.
Fruits grow to their full size (ca. 500 g) every fall, and each fruit can bear up to 300 seeds per fruit. Osage orange has traditionally been used as an insect repellent and as a home remedy for pest control. Fruit extracts and extracts of the bark, seeds, leaves, and roots, as well as the two major isoflavone constituents of the fruit, osajin and pomiferin, were reported to possess a number of biological activities. Some of the reported activities include insect repellant, antimicrobial, anti-inflammatory/antinociceptive, antitumor, cardioprotective, and cholinesterase inhibitory activities. Osage orange isoflavones, especially pomiferin, also have marked antioxidant activity and have been shown to inhibit lipid peroxidation and to reduce free radicals, reactive oxygen species, and other unstable molecules. At present, there are no osage orange-based dietary supplements available on the market, but its potential has been suggested. Biological evaluation of semisynthetic osajin and pomiferin analogues, iso-osajin and iso-pomiferin, has also been attempted by Orhan et al. Being edible by squirrels, horses, and other animals suggests that osage orange is safe. Nevertheless, the toxicities of the different extracts have not been fully established. References removed for readability
HPLC Determination of Isoflavone Levels in Osage Orange from the Midwest and Southern United States
Ketur Darji, Cristina Miglis, Ashley Wardlow, and Ehab A. Abourashed
You often hear about herbal or Ayurvedic remedies for a whole host of ailments. I won’t talk about homeopathy because that’s too easy to dismiss. Pharmacognosy is the study of medicinal compounds derived from plants. You might hear about ethnobotany and phytochemistry in descriptions of pharmacognosy. Ethnobotany is the study of plants as they relate to culture, predominantly indigenous cultures. Phytochemistry is the study of the chemistry of plants (cue elderberry joke). It’s pharmacognosy that’s used to determine if a “traditional” remedy has any scientific basis. Typically ethnobotany is used to find some candidate plants. I have a friend in this field and if I recall correctly, there was a time when western scientists would go to the jungle (for example) and take plants without working with the local government. Relationships soured and some areas are off limits. I believe most of the studies now have agreements with the local governments and indigenous people so that it’s not the new version of pillaging their gold, i.e., if a derived compound leads to a blockbuster drug, they’ll get a slice of the pie.
After a candidate plant is chosen, Maclura pomifera in this case, compounds are isolated from the bark, fruit, flower, leaves, and roots. Since this is a tree, I’m guessing the roots were not tested. Typically the compounds will be separated based on water solubility. You might know that a lot of old remedies are made with ethanol, i.e., a tincture. Then each compound is analyzed for it’s chemically properties, e.g., structure and then against a host of in vitro assays to scan for potential medicinal uses, possibly beyond what was learned from ethnobotany.
The paper referenced above (which is behind a paywall) used high pressure liquid chromatography (HPLC). Chromatography comes from the Greek chroma “color” and graphein “to write”. There are different types of chromatography but each results in a chromatograph. Its name derives from its early use in separating pigments in plants. Probably using thin layer chromatography (TLC), where a plate or piece of paper is used in a solvent. The sample is placed on one end of the plate/paper and the individual compounds separate as it travels through the solvent. This can be due to size, charge, or polarity. In HPLC, there is a mobile phase and stationary phase. Typically the stationary phase is made of special porous micron-size silica beads and is packed into a steel column. The mobile phase is typically a solvents like toluene or acetonitrile. When the mobile phase is less polar than the stationary phase it’s called normal phase liquid chromatography. When that’s reversed, i.e., the mobile phase is more polar than the stationary phase, it’s called reverse phase liquid chromatography. The reference above used reverse phase.
For a long time the effluent from HPLCs were connected to a UV-Vis (ultraviolet and visible range) spectrophotometer. Each compound has a preference for each phase (mobile or stationary). They travel through the column at different rates and they have different spectra. That’s how you get the chromatograph. In the old days, the spectrometer was tuned to a single wavelength, typically where your compound of interest has a peak. Later, with photodiode array technology, the whole spectrum for each compound was acquired, resulting in a 3D chromatograph. However, now, HPLC detectors are predominantly mass spectrometers (MS). So you get the mass of each compound as it elutes from the column.
Going back to pharmacognosy and Maclura pomifera. Two of the main compounds isolated are pomiferin and osajin . In another study pomiferin was isolated and had an inhibitory effect on the growth of 5 tumor cell types.
Pomiferin, histone deacetylase inhibitor isolated from the fruits of Maclura pomifera.
Son IH, Chung IM, Lee SI, Yang HD, Moon HI.
Bioorg Med Chem Lett. 2007 Sep 1;17(17):4753-5. Epub 2007 Jun 26.
When ScienceSunday first started, Robby Bowles and Allison Sekuler had an idea that photographers could share interesting pictures with real scientist (Robby and Allison) and the Science Sunday team could either answer a science question or add some science goodness. Sunday was chosen because we do this in our “spare” time and Sunday seemed like the best day for spare time. So the hashtag #ScienceSunday was born, followed by the page. As the popularity of the hashtag grew, more curators were added: Rajini Rao, me and then Buddhini Samarasinghe. The hashtag and page continued to grow. So we often have guest curators to help out. Unfortunately a lot of people see a trending hashtag and use it because they think that people won’t want to see their post/photo otherwise. The curators have to sift through a lot of junk to find the good stuff. So welcome Aubrey Francisco our new co-curator with some good stuff. The pictures below were from my trip to the Fox River, Silver Springs State park, yesterday. Enjoy the rest of your #ScienceSunday and don’t forget to tag one of the curators when you have a science question or some science to share.
I was working on my post for #ScienceSunday about medical image visualization and I ended up down a rabbit hole. I hope to finish writing this evening. In the meantime, tell me what science you see in this image. I changed it to my profile pic because it’s me but what else do you see?
I came across an article in Psychology Today discussing the Cambridge Declaration on Consciousness. You can read more about the declaration in the links below. Basically a group of scientists met in Cambridge and proclaimed their support for the idea that some animals have a consciousness. Don’t get carried away and confuse that with intelligence. Also the declaration doesn’t say anything about the treatment of animals. I was a bit annoyed that the Psychology Today article kept mentioning abuse, as if to stoke the ire of the animal rights activists. It’s interesting that the article mentions the Animal Welfare Act. It is true that there are some animal studies that the general population might find unsettlingly. However, there are so many regulations on what you can and cannot do when it comes to animal research, that I find the term “abuse” to be disingenuous. Contrast that with the article from io9.
I’m in total agreement that some animals have consciousness and that they should be treated humanely. Here’s an excerpt from the declaration.
The absence of a neocortex does not appear to preclude an organism from experiencing affective states. Convergent evidence indicates that non-human animals have the neuroanatomical, neurochemical, and neurophysiological substrates of conscious states along with the capacity to exhibit intentional behaviors. Consequently, the weight of evidence indicates that humans are not unique in possessing the neurological substrates that generate consciousness. Nonhuman animals, including all mammals and birds, and many other creatures, including octopuses, also possess these neurological substrates.
I’ve talked about birds already (see the PET link below). The rest of this post will focus on something I shared back in December 2011. I shared it privately as I was new to G+. So I’m redoing it here. The image below is a screen capture of a study by a group at the The University of Chicago The video is in the link below, Helping your fellow rat.. Bartal et al showed that rats can demonstrate empathy by having a free rat rescue his or her cagemate, which is placed in a plastic restrainer. Once the rats learned to open the restrainer, they only opened it if there was a cagemate in it, i.e., if it was empty or had an object inside they left it locked. Also, when presented with a locked cagemate and a locked piece of chocolate, the free rat would unlock both and share the chocolate. That’s better than many politicians. Rats were initially startled by the door opening. In later repeated tests, the rats were no longer surprised by the door opening, i.e., it was an expected outcome.
The data suggests that females are more empathetic. All of the females became door openers while only 70% of the males opened the door. Also, the females learned to open the door sooner than the male rats.
Combined with the bird studies, there is mounting evidence that animals have more going on in their brains than some people think.
Here’s another example of some interesting science that doesn’t need any hype. The news blurb is titled Injectable Oxygen Keeps People Alive Without Breathing and was shared here: http://goo.gl/xjmeE4 I promised Rahul Roy that I would follow up after reading the full journal article. Notice the title on the journal article is less sensational, Oxygen Gas–Filled Microparticles Provide Intravenous Oxygen Delivery JN Kheir et al. Sci Transl Med 27 June 2012 http://goo.gl/9tN6yx Techandfacts.com actually did a decent job reporting the science. The title is a little hyped but not bad. I’ve certainly seen worse, e.g., Bench to Bedsidehttp://goo.gl/xudsu
So what is this article about, what’s the science?
❤ Lipidic oxygen-containing microparticles (LOM)
Dr. Kheir et al created microbubbles or LOMs to deliver oxygen when patients have difficulty breathing. This is an important part; it is not a blood substitute. It is not intended for trauma involving blood loss. We’ll get back to that later. What is LOM? When you make a vinaigrette you notice that oil and water don’t mix. You can shake/whisk the mixture or use an emulsifier (like mustard) to make an emulsion (a mixture of two liquids that normally don’t mix). Micelles are formed when a molecule has a hydrophobic part (doesn’t like water) and a hydrophilic part (likes water) and it’s placed in a liquid. If the liquid is water, the hydrophobic parts try to escape the water and end up on the inside of a sphere with the hydrophilic part on the outside. So the lipidic part of LOM is used to make micelles with oxygen inside. They use sound waves (via a sonicator) to disrupt the micelles enough to trap the oxygen inside of them. A red blood cell is 7-8 µm in diameter and the LOMs are 2-4 µm so they have no problem getting through the capillaries.
❤ O2 delivery vs. O2 carrier
So why is this good for short term use when there may be an issue with breathing but not in a trauma, blood loss situation? The LOMs are injected into the bloodstream where they can quickly oxygenate the blood. See the beaker of blood before and after adding LOMs (via the journal article). As the oxygen leaves the LOMs and saturates the hemoglobin in blood, they shrink. Think of a balloon releasing oxygen. The “deflated” LOMs cannot be “re-inflated” in the bloodstream (remember the sonicator was needed to get the oxygen in). You can see a deflated LOM in the lower left of the cartoon. Also carbon dioxide is not removed. In the short term this isn’t an issue. If this were needed for longer use, the CO2 would build up and make the blood acidic.
So what’s the difference between O2 delivery and an O2 carrier? LOMs are an O2 delivery system. Oxygen (or carbon dioxide for that matter) does not go back to the LOMs as they circulate. There two types of artificial oxygen carriers: hemoglobin based and perfluorocarbon (PFC). The LOMs are closer to PFC formulations.
❤ Perfluorocarbon (PFC)
A perfluorocarbon is an organic compound made up of carbon and fluorine. Emulsions of PFCs can be made that carry oxygen. Early on the emulsifiers used in PFC emulsions caused allergic reactions in people. The biggest problem with PFCs in the context of artificial blood is that the oxygen carrying characteristics require high oxygen content in the blood in order to release the oxygen. If you look at the figure below (http://goo.gl/csOsnk) you can see that you need a higher partial pressure (pO2, oxygen concentration) for the PFC relative to blood to release oxygen. Here’s a video that shows a mouse breathing liquid PFC. You might see other videos incorrectly state that it is a mouse breathing water.
So what makes blood or hemoglobin so much better than PFC for oxygen carrying? A little compound called 2,3 diphosphoglycerate (2,3 DPG) is the key. It’s an allosteric effector. Allos from Greek means other and stereos means space. So an allosteric effector changes the shape or folding of a protein when bound or unbound. When 2,3 DPG is bound it shifts hemoglobin to the low affinity state for oxygen, i.e., releasing it more readily. It’s increased levels help in conditions of low oxygen/blood, e.g. traumatic blood loss.
One other tidbit, these microbubbles aren’t new. They have been used as contrast agents for ultrasound imaging, which I’ll talk about in another post. I can also talk more about hemoglobin based oxygen carriers in a future post if there is interest.
Science outreach is one of the reasons I spend a lot of time on G+. It’s one of the reasons I care about G+ as a platform. If you follow me, you might have seen me bellyache about getting notifications from people I don’t have circled and how that interferes with my science outreach (mostly curating #ScienceSunday ). Today I’m going to share an example of why it is important to me for people to be able to notify me about science.
❒ Science Outreach
Michael Davis read an article in TIME magazine (http://goo.gl/elCMSa) and wondered if the claim that chemotherapy would be a thing of the past was true. So he mentioned me in his post and I looked at the article and realized it was another case of sensationalizing some exciting research. The fact that Michael follows my posts enough to trust my opinion about cancer, really pleases me. It is very fulfilling to be able share my knowledge with people who want to learn. It’s interactions like this that make me tolerate any negativity on G+, e.g. trolls. It’s people like Michael that make me want to post more science and get better engagement on my science posts.
❒ Sensational Headlines
The TIME article discusses a recent phase 1-b clinical trial for a new cancer drug. I explain more about it below. The claim that traditional chemotherapy will be a thing of the past is not only premature, it’s also misleading. There will still be cases where current treatment (surgery, radiation, and non-targeted chemotherapy) is an appropriate course of action. Say for example, someone receives a PET scan and it reveals tumors throughout the patient’s body. It doesn’t make sense to biopsy all of those tumors and it is possible that all of those tumors aren’t genetically identical. So some of the advanced targeted therapies would not be applicable. See Buddhini Samarasinghe’s post (The Signatures of Cancerhttp://goo.gl/LmyS0z) to get a sense of the variability in tumors. 21 distinct mutational signatures are discussed.
Many of us have posted about sensationalizing headlines before.
A quick glance at the article suggests they are really trying to say that broad spectrum (to borrow the terminology from antibiotics) are being phased out in favor of targeted therapies. This isn’t really new or news. One example they give is imatinib or Gleevec. Imatinib targets a specific type of enzyme, a tyrosine-kinase inhibitor. You can read the Wiki on it or I can write more later. The important thing is that imatinib builds on knowledge from previous tyrosine-kinase inhibitors like sorafenib, which has an antiangiogenic mechanism. It targets new blood vessels, which the tumor creates. As far as the HIV comment, check out Rajini Rao’s post (http://goo.gl/q4Bk7) if you haven’t already. There’s comments about other gene therapies in there too.
Backing up a little bit, a protein kinase, is an enzyme that’s involved with a process called phosphorylation, where a phosphate group is transferred from a high energy molecule to a specific substrate. A tyrosine-kinase is just a type of kinase where the phosphate group is attached to tyrosine (an amino acid). Phosphorylation is often described as a molecular on/off switch. When a protein is phosphorylated or dephosphorylated it can be switched from on to off or vice versa.
So the new drug in the article, ibrutinib, is a Bruton’s tyrosine kinase (BTK) inhibitor. BTK is essential for the proliferation of chronic lymphocytic leukemia cells. As mentioned in my comment above, it builds on prior knowledge of kinase inhibitors. In my opinion, it’s not a revolutionary breakthrough. It’s an important and fantastic step forward. It is not a silver bullet.
❒ PDX
An example of another targeted drug that’s been around for a while is tamoxifen. It targets estrogen receptor positive (ER+) breast cancer. For breast cancer, a biopsy is often taken when there is a suspicious lesion in a mammogram, ultrasound, or MRI. The biopsy might reveal that the lesion is in fact cancer and is ER+. In that case it is reasonable to try tamoxifen. My point here is that targeting is not new, even though the targeting is getting more specific.
A colleague is working on an exciting project called PDX, patient derived xenograft. What that means is that a piece of the patient’s tumor is taken to the lab on ice and implanted in immunocompromised mice. That’s called a xenograft, i.e. grafting from different species. Typically cancer research is carried out on tumor cell lines that are well characterized and have been around for a long time. The problem is that some of those cell lines don’t fully resemble the tumor in the patient scenario. The PDX project has the potential to better model the patient scenario as we know exactly where the tissue came from. More importantly, it allows us to better target that specific tumor. That’s exciting work without making it sensational and it won’t be a silver bullet either as some tumors might not grow in a mouse.
Image source:
V.A. “Vinnie” Musetto “Headless Body In Topless Bar”
I’ve been busy with visiting family for the 4th of July holiday. You’ve probably noticed my stream is stagnant. Since I don’t have time to write up a decent post, I’ll piggyback on Buddhini Samarasinghe’s excellent post.
G+ is a great place to meet people with similar interests. I’ve heard several times that FaceBook is for keeping in touch with people you already know and Google Plus is a place for meeting people you don’t know, who have similar interests. For me that’s Science. I’m a scientist and I’ve had the pleasure of becoming friends with other scientists here that share a passion for science and science outreach.
Whether it’s curating ScienceSunday, posting about science on our own, or fighting pseudo science/anti-science, there is a group of real scientists that work hard on this endeavor. Counteracting the sensationalizing of science is part of what we do.
Thanks Buddhini Samarasinghe for an excellent post that I agree with wholeheartedly. Here’s my favorite post for dealing with a cancer story that was blown out of proportion.
Two years ago, I signed up to G+ and was thrilled to discover so many scientists and science advocates on here – I found my kind! From those early days, we built a community, from the ground up, made of people who were passionate about communicating science and battling anti-science. Over time, we gained enthusiastic support from the public, and our followers on G+ grew, along with the engagement we received from the content we produced. Fascinating topics, insightful discussions, the occasional swatting of the pseudoscience troll, these were all things that brought us closer together. Pages and Communities sprang up, all with the common goal of science outreach and public education and I am so proud and happy to be a part of that. To that end, ScienceSunday and Science on Google+: A Public Database are excellent resources for any newcomers.
As a scientist, communicating science comes with a responsibility to be honest. When I write a science post, I do it because I read a paper that made me go “wow, that is so cool! I want to share that with people!”. My goal is not to hit What’s Hot, or to get more followers, or to become popular, or to increase a Klout score or whatever. I don’t care about those things because they are side effects.
Because of this, I don’t sensationalize my posts to become popular. I strongly feel that the science I write about is already pretty damn sensational. I don’t need to lie to you, the public, to make you excited about it, because I hope that my science writing skills can translate the jargon from the research so that you are excited about the science itself.
Sensationalizing scientific discoveries is patronizing. It implies that you, the public, is too stupid to understand or care about the science, and I need to deliver it in a form that you will consume easier. This is lazy, and ultimately doesn’t really educate anyone about the scientific discovery; it just spreads misinformation.
Sensationalizing science also leads the public to have false expectations about the science. A sensationalized title such as “Scientists Have Grown a Fully Functional Liver from stem cells” might hit What’s Hot, but is an outright lie. It leads the public to expect ‘fully functional livers’ to be made available to transplant candidates within months and years, whereas the reality is far from the case. This is not the fault of the science, or the scientist.
Misinforming the public to popularize science does not popularize science; it hurts science. The science out there is already so amazing, we don’t need to make it something it’s not. I understand that it’s not easy for everyone to always read the original paper and understand it, let alone convey the findings in a manner that the public can understand, but sensationalizing it to make people take notice is disingenuous and lazy at best, and harmful and detrimental to our collective goals of science outreach at worst.
If you have me circled, I won’t lie to you. I will do my best to share the research that I think is exciting, in a jargon-free manner that I hope you can understand, and be available to answer any questions you might have about it, or find other scientists who could answer you. You can expect to read about things like radioactive bacteria shrinking tumors (http://goo.gl/FhPeM), the evolution of snake venom proteins (http://goo.gl/qZHcF) or how a compound in breast milk could be used to treat MRSA (http://goo.gl/RQGv5) if I am in your circles. I am here to communicate science and to make you as excited about it as I am. I don’t need to sensationalize something that is already sensational.
Thanks Tommy Leung, Rajini Rao, Hedwig Pöllöläinen and Brian Koberlein for inspiring this post. It’s something that was on my mind for quite a while, and you guys were awesome catalysts 🙂
Steve Mould explains that magenta or pink is created because we only have 3 different cones for color vision: red, green, and blue. It’s not surprising that most tv’s and photographs use the RGB colormap, i.e., only combinations of red, green, and blue.
In my research we often use different color spaces. I’ve mentioned RGB (red-green-blue). Some journals ask for figures in CMYK (cyan-magenta-yellow-black). But have you heard of CIE L*a*b* (CIELAB)? It’s an interesting color space. It can be helpful for image segmentation. http://en.wikipedia.org/wiki/Lab_color_space
There is a lot of concern about the decline in bee colonies. As most people know, if there are no bees, then many crops will suffer as they need the bees to pollinate them.
Wenfu Mao, Mary A. Schuler, and May R. Berenbaum, from the University of Illinois, recently published in PNAS that feeding high fructose corn syrup, as honey is taken away from bees, might be contributing to Colony Collapse Disorder. Since the 70s, corn syrup has been given to bees in colonies as their honey is harvested from them. Mao et al found that the bees immune system was stronger when exposed to p-coumaric, an enzyme that turns on detoxification genes. It’s found in pollen walls.
Reference:
Researchers find high-fructose corn syrup may be tied to worldwide collapse of bee colonies
Most of the focus has been on neonicotinoids, which are a class of neuro-active insecticides chemically related to nicotine. Pyrethroid is a compound used in commercial insecticides that is similar to pyrethrum, which is the active ingredient in Chrysanthemum flowers. Chrysanthemum flowers were used to kill lice for centuries. http://en.wikipedia.org/wiki/Pyrethroid
In this article by Frazier et al, they explain how neonicotinoids aren’t the sole problem. The amount of neonicotinoids found does not add up.
This is in contrast to pyrethroids which were found in 79.4% of samples at 36-times higher amounts than the neonicotinoids, on average.
Pesticides and Their Involvement in Colony Collapse Disorder
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