ellestra: (charlie jade)
LHC was supposed to be back in operation after two years of upgrades but it short-circuited during booting so we'll still have to wait for that dark matter explanation a little longer. They need to opposite of vacuum it first by flushing it out with high-pressure helium gas.

For the first time since MIR there will be someone living in space for a year. Or rather two someones. One is Russian and the other is American and a part of real life re-enactment of the famous identical twins experiment. The one when one stays on Earth while the other is in space. Identical twins and space. No near relativistic speeds this time so age difference will be unnoticeable but there are plenty of other things to learn. The last cosmonaut in this mission crew will be only staying for standard 6 months but that will allow him to become the person who spent the most days in space ever nevertheless.

Curiosity discovered another compound that's connected to life as we know it - nitric oxide. Most people think about it as laughing gas but it only has that effect because it's an important signalling molecule that triggers a lot of metabolic pathways. It can also be the result of lightning or meteor impact so it doesn't mean much by itself but might be also another clue in Curiosity's search for life. Meanwhile her landing marks fade.

While Curiosity is still only beginning her journey Opportunity has just finished a marathon. It's been more than 10 years and 42km and it's still going. Maybe xkcd is right. Maybe she's marking what hers. Unless amnesia gets her first.

I thought that starfish ripping themselves apart were horrific enough but now octopodes are eating their own arms. In next Syfy movie this will be an alien virus that just goes up the animal kingdom all the way to humans. The trick is to invent even more horrific form of self mutilation than those already described.

Graphene light bulbs because what is leaving in the future worth without it being made of science fiction materials.

Artificial ants working together just like the real ones
ellestra: (slingers)
It turns out the strangest thing about black holes isn't the event horizon that nothing, not even light, can escape. It's not their mass. It's their density. It turns out that adding mass to a black whole doesn't work the same as normal matter. When you add mass to black holes the radius of the black hole grows at the same rate and that means the volume gets bigger to the 3rd power which means the density become less by the cubic root. A black hole with the mass of 387 million of our suns would have the average density of water. So Interstellar was right to pick a gargantuan black hole. Not only you don't get spagettified (pulled apart when you are falling into it) but you may also find inside like a big swimming pool.

The first flexible brain implants are being developed to replace metal ones. They will not only be able to deliver electric impulses but also drugs and record brain activity at the same time. This is how the Matrix starts.

What makes biology work is sequence - just like DNA's ATGC - that codes the information and structure - the 3D folding. It's important for DNA as it influences whether the information in it can be used or not (the inactive parts are folded and inaccessible) but it's most important for the enzymatic activity. Ribosomal and transfer RNA can only produce proteins when they are folded into right shapes. Proteins can work the same even with sequence change (amino acid substitutions) if the shape (and catalytic centre) stay the same. Temperature destroys that shape and many proteins cannot go back to the same shape. This is why fever above 42oC is so dangerous. This is what happens to boiled eggs. But now a way to unboil egg whites has been developed by liquefying the whites with urea (main ingredient of pee) and then use vortex fluid device to make them fold back to right shape. The most important part is that it can be used for many other proteins. Like the ones used in medicine.

Disneyland became a ground zero for a measles outbreak in California and it's due to the rising numbers of unvaccinated children that serve as repositories of the disease. It can than spread to people with lowered immunity, too young to be vaccinated and the ones who lost their immunity - like elderly as it lowers with time. A lot of those populations are particularly susceptible to complications. There is certain level of disgust I feel for people who are wilfully ignorant and defend their ignorance even at the cost of other people health and lives. And they defend it as a safe choice and protecting their children. Even though they really endanger them. But if it was just them and their children it'd be just wrong. The despicable thing is the part there they also endanger others - all the people who would otherwise never got sick. This is one thing I wish people who do this could be sued for endangering society and costs of healthcare.

It's not only El Niños that is going to happen more frequently now but also La Niña. The Pacific hot/cold water oscillation leads to extreme weather patterns all over the Pacific basin and influences global weather patterns so they are going to become even more unpredictable than they already are.
ellestra: (slingers)
It's the end of the year and it's time to sum up this year in science and that's a much better story than news. Multiple sites have than their pick of th best and most important science and technology stories this year - from weird to futuristic, from space to new element and quark combinations, from new biological organs to synthetic chromosomes and from Nature to Science. And Wired. And New Scientist. And Scientific American.

There are things that only just happened so I didn't get a chance to write about them yet and they didn't land on any list - like the strange fish that lives 8 km deep in the ocean and looks more alien than most science fiction creatures ever will (although it kind of reminds me of Falkor). Scientists learning how to speak monkey. Venus is hell (hot, hot, hot and full of sulphur) but NASA Research Center has plans to put cloud cities on it high in the Venus atmosphere where it's not too bad - apparently living just above hell is doable just as long as you don't fall. And you can name a crater on Mercury.

For me the two most important things that happened in science was - one - all the progress at organ replacement and prosthetic - from new ways to create stem cells and 3D printing organs and growing replacement ones in a vat - like vaginas to creating new, better fitted, cheaper and cooler, prettier 3D printed prosthetics and reconecting nerves in paralysed to advances in cybernetics that allows for mind-controlling the artificial limbs and feeling the objects you touch (bionics is real and cyborgs are no longer sf). Two - all the comet stuff - the Rosetta mission most of all - from the Philae drama to water that's different from the one we know (so comets are not the source of our oceans) - but also the Siding Spring pass of Mars.
ellestra: (tiger)
Every year Science organises the Dance Your PhD contest. Here are all the finalist from Chemistry, Physics, Biology and Social Sciences categories. And this is the winner:


Science isn't always easy to portray in art and it's rarely accurate but Interstellar had it's own science advisor Kip Thorne is Feynman Professor of Theoretical Physics at the California Institute of Technology, Pasadena design some of it's special effects. New Scientist has spoiler-free guide to the science of Interstellar. Space ships and science - two things I really like together.

And here is first teaser trailer for season 3 of Orphan Black - just in time for Orphan Black Friday
ellestra: (telamon)
All the way back, soon after I got sick, the news broke about the impossible engine. This is the kind of thing that sounds like ure science fiction and almost everyone couldn't believe that it would work (they also didn't believe Chinese scientist who built something similar first) but the nit was built and it's working (as far as I know noone disproved it yet). It uses the virtual particles - the ones that came to existence and almost instantly disintegrate due to some laws of quantum physics - to push the objects around. It's almost like using magic - except it works. It's not very useful right now - you get very little for the amount of power you need to feed it but you don't need to bring fuel with you which makes everything easier - that fuel mass is always a problem. However, the best part for me is that there are still things that can surprise us like this. There might be hope yet for our space dreams.

The panspermia theory has long been one of the explanations of how life could've started on Earth. We know that there are some organisms able to survive in outer space but here are some that got there seemingly on their own and are still viable even after long exposure. Russian cosmonauts have found life on the outside of the International Space Station. They were pretty shocked to discover what seems to be sea plankton on the exterior of the station that is apparently being lifted all the way there by atmospheric currents. And it's somehow surviving there.

A 24-year-old Chinese woman does not have a cerebellum. Cerebellum is a large brain structure (see photos in the link) that is mainly responsible for motor control and also controls some cognitive functions. She had some balance problems since she was a child but was only diagnosed when she finally went to hospital complaining of dizziness and nausea. It's the ninth case in medical history and it shows how amazingly plastic our brains are as other parts of the brain have managed to pick enough of the cerebellum functions to allow her to live relatively normal life.

On the other end of scale transplant of olfactory nerves helps a paralysed patient regain partial movement. Doctors in Poland and scientists from England have used harvested culture of olfactory ensheathing cells (OECs) and olfactory nerve fibroblasts (ONFs) to reconnect spinal cord severed by injury. Unlike most of the nerve cells olfactory ones need to grow new axons all the time to connect to new cells in our nose. This made them perfect candidates for growing new connections. The doctors have harvested olfactory bulb during brain surgery and cultured the cells. Then they had removed glial scar tissue and then transplanted the cultured cells into spinal cord stumps above and below the injury site, where an 8 mm gap was bridged by four strips of autologous sural nerve. After two years patent regained some feeling and function - he went from complete paralysis to being able to walk with leg braces and a walker.
ellestra: (winged)
One of the reasons I've been slacking on science news is because I know I should write about Ebola and that's not a fun subject. I started this back in July but then got distracted by my own diarrhoea problems and thinking about the version with your own liquidated organs coming out wasn't especially appealing. I've been avoiding it since - hoping a little that it'll get under control before I do - but it is an important example of epidemic outbreak and what works and what doesn't for controlling it. We are not doing all that well but luckily for us Ebola is very infectious but not very contagious. This makes it perfect for this kind of test. Its horrifying symptoms have long been beloved by all the thriller writers so everyone sort of knows to be scared but it is pretty hard to catch. I mean it's easy to get infected but it's you have to be very close to the sick people so it's relatively easy to stop it from spreading. It's not like some other diseases that we vacinate for where just breatheng the same air or being in the same room a sick person was in couple of hours before can make you sick.

Unfortunately this current outbreak started in some of the poorest countries with health systems thatdon't have enough resources to deal with it. The wide spread of the disease is a consequence of that. There was a shortage of even such basic things as gloves and rumours that led patints to escape qaurantine and it spread. Howeve, usually modern methods of disease control prevail - this how Nigeria stopped the outbreak.

There is also panic because it reached USA and Europe but you should remember that we are still pretty safe even though the prognosis is getting worse and worse for the worse affected regions. However if you are outside of West Africa there is no reason to panic.

But one good thing about that artificial panic is that it makes people pay attention and that makes the resources to deal with it more easily available. Including allowing the administration of experimental drugs. This doesn't happen very often as there are important reasons for testing them as long as we do but when chance of survival is pretty slim side effects become acceptable risk. Especially, in this case when we don't have much so we are throwing at it whatever we got. But sometimes even this kind of danger is not always enough - there is a vaccine in the works but it might be delayed because of the patent dispute.

Let's hope all this noise will result in a vaccine and improved systems dealing with outbreaks. In a perfect world malaria will be next (or can we at least make pundits scared of it enough for people to care?)
ellestra: (slingers)
In celebration of Yuri's Night tomorrow this is a science post.

There is going to be a series of Lunar eclipses - roughly every 6 months - and the first one will happen this Monday night. By fluke, Monday is also the date of Mars’s closest approach to Earth, when our neighboring planet should appear larger and brighter than usual. Both Americas will see it whole early on Tuesday - the lunar eclipse will start around 2 a.m. EDT and and around 5 with totality, called the umbra, at 3:45 a.m. EDT.

The LHC discovered a strange new particle known as Z(4430). This new particle is about four times more massive than a proton, has a negative charge, and appears to be a theoretical particle known as a tetraquark. There were previous indications of this state of matter but LHC caught ten times more events then anybody else so we are more certain this is something that can exist. Due to strong force rules quarks cannot exist outside particles - they have to be together with other quarks to create a particle that has neutral colour charge. So baryons - protons and neutrons - have neutral colour because they contain quarkks with all three colour charges (blue, red and green) and mesons are neutral because they have a quark with colour charge and quark with a anti-that colour charge.
Under the rules of the strong force, there are other ways quarks could combine to form a neutral particle. One of these, the tetraquark, combines four quarks, where two particles have a particular color and the other two have the corresponding anti-colors. Others, such as the pentaquark (3 colors + a color anti-color pair) and the hexaquark (3 colors + 3 anti-colors) have been proposed. But so far all of these have been hypothetical.
Now we are starting to capture those theoretical particles and we even know what they are made of - Z(4430) is made of a charm, an anti-charm, a down and an anti-up quarks.

Four teenagers were successfully implanted with lab-grown vaginas. The surgery was done 5 to 8 years ago and the organs are are working normally in four teenage patients who were among the first people to receive such an implant. All of them were born with a rare genetic condition - Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome - in which the vagina and uterus are underdeveloped or absent. The The vaginas were grown in a lab from patients own cells from small sample of vulvar tissue. The cells were grown on two sides of scaffold to get the right shape and the two different cell types vaginas are made of - muscle cells and vaginal epithelial cells. When the organs were ready the doctors implanted them connecting uterus with surgically made cavity. And now they work. Hopefully, all the people who need a vagina will have access to this procedure soon.

This Jason Barnes playing drums with his new metal prosthetic arm
ellestra: (tiger)
Everyone is talking about the Jade Rabbit's goodbye messages. China's first Moon rover is malfunctioning and most likely won't survive the night (they last 2 weeks and temperatures drop to -170oC). Like it is in style for the rovers now it has its own twitter feed where it gets personified so we would care. And now they make us watch it die. I blame xkcd with the Spirit cartoon Randall Munroe started the whole tearjerker thing.

But the real horror is happening in the deep. The starfish are suffering from a sickness that makes them rip themselves apart. The arms start crawling in the opposite directions until the body breaks and insides spill out. This is the scariest thing I have heard about and I read a lot about biology that includes parasites bursting out of bodies and zombiefying creatures. Or wearing bodies of your victims as armour. Or becoming sperm dispenser for the first female of your species you encounter. You know nature.

NewScientist has an interactive tool showing temperature changes all over the world. Spoiler alert - it's warmer almost everywhere. Excapt few ocean spots and some regions of Antarctic the planet just gets warmer. For most of Europe, including Poland, it's little over 1oC. The warmest places are Amazon jungle and all the very cold north - Siberia and Canadian Arctic. Poor polar bears.

Turning differentiated cells back into stem cells isn't easy. Stem cells can become any other type of cells even a whole new organism but once they become differentiated there are changes in the structure of chromatin that seal the cell fate. It changes shape, metabolism and can only divide a set amount of times before dying. So far making them go back to the stem cell pluripotent state has been mostly unsuccessful. This means that both cloning the adult organisms and getting stem cell therapies going has been very slow. Including the controversy about harvesting and using embryonic stem cells.

However, recently scientist in Japan crated a method of reversing cells to the stem cell state by placing them in place the cells in a stressful situation, such as an acidic environment. Cells was exposed to a "sub-lethal" acidic environment, with a pH of 5.7, for 30 minutes. Some cells died but the rest started, slowly, over time of several day to show genetic markers of pluripotency – many of which are also seen in embryonic stem cells. It was not only more successful but also faster that any previous method. The method so far worked on every type of cell - from liver to neurons - and on all tested mammals - including primates. What's more - if the cells are placed with growth hormones they can start multiplying exponentially and it may lead to a whole new organism in right conditions and be an alternative and more efficient method of cloning.
ellestra: (tiger)
Prof. Andrzej K. Tarkowski was just awarded Polish Science Fundation Prize in 2013 in the life and earth sciences, for discoveries explaining the fundamental mechanisms responsible for the early development of mammalian embryos. I just listened to his interview on Polish public radio and it brought back so many great memories. He was teaching biology of development on Warsaw University's Faculty of Biology and his lectures where one of my favourites. I had to come early all the way to city centre where department of Animal Physiology was located to the attend his lectures and then wait couple of hours before the labs started but I came anyway. Attendance on lectures is not obligatory in Polish universities - you just have to pass the final exam. Only attendance on labs is checked but lectures are not obligatory - you just have to learn the material. I went to his lectures anyway because they were awesome.

All the information about how you can separate zygote into separate cells that will result in separate organisms and how chimeras can be made by combining multiple zygotes together from the man who pioneered this research. Back then no one knew they would be even viable and now we know both happen in real life in animals (including humans - I wrote before about human chimeras). They also learned that masculinization was dominant because mice chimeras made of male and female zygotes combined together resulted mostly in male mice. Now we know that this is how sex differentiation works. SRY gene on Y chromosome triggers production of testosterone that turns embryo male before it goes through the default development into female. It was all fascinating and if I wasn't set on being geneticist (and not fond of killing animals) I would go into embryology.


One of the big biology discovery talked about in past few weeks was the publishing of the findings of the University of Pennsylvania scientists that the brains of men and women are connected in different ways. Most of the connections in male brains are between front and back and in female are between the hemispheres. Structural and functional differences has been shown in many previous research but this also shows differences in connections between brain structures. However, as it always happen when you mention differences between groups of people, this discovery led to people just run screaming how all the stereotypes about men and women are totally proven by science. They are not.

One - we are still not sure what is cause and what is effect. Brain's connections are highly flexible and change through life and they can be trained by what we use our brains for and changed by our experiences. The tasks that women and men are better might be the tasks they are the trained to do better. Two - we don't really know how (or even if) those differences in connections influence behaviour and brain function. The fact that man usually only have speech centre in the right hemisphere doesn't mean that there isn't a lot of them who talk a lot and write speeches.

As BBC article says:
"One thing that remains unknown is what is driving these differences between the sexes. An obvious possibility is that that male hormones like testosterone and female hormones like oestrogren have different affects on the brain.

"A more subtle possibility is that bringing a child up in a particular gender could affect how our brains are wired."


The oldest human genome sequenced is from 400,000-year-old femur from Spain and it's mitochondrial genome is Denisovan genome. It was a surprise as until now the Denisovans were only known to have lived much more recently in southwestern Siberia. Ancient DNA researchers were expecting bones to be more closely linked to Neanderthals than to Denisovans and the bones from that site were considered to be Neanderthal bones. However, this is just mitochondrial DNA - it is much easier to find enough of it to sequence as it so much more copies of it then nuclear DNA. You can only inherit it from the mother so that means that if there was interbreeding between Neanderthal and Denisovan populations the Neanderthal who this bone belonged too might've just had a direct female line Denisovan (or Denisovan-like) ancestor. I'm mostly still in awe that they managed to sequence anything that old.


Using viruses to insert sequences into genome is a one of the ways we tried to do gene therapy. It even works sometimes. But the changes are not inherited. Mammals only have small amount of the cells that are used to make gametes (cells used for reproduction) - changes to any other cells cannot be inherited. So this time they introduced new genetic material via a viral vector into the sperm of mice and it led to the presence and activity of those genes in the resulting embryos. This new genetic material is actually inherited, present and functioning through three generations of the mice tested. This means that the genetic diseases can be cured in future generations. It is very hard to change every cell in a grown up organism but if you could just change gametes you wouldn't have to worry about your children inheriting the disease. This may also be the first step to designer traits in offspring. It's not going to be flashy (nor as evil) as pulp sci-fi makes it too be but this is what the future was supposed to be like and we may need to start to think how we are going to deal with it.
ellestra: (tiger)
I was so busy at work and so occupied by Doctor Who outside of it that I only learned today that Frederick Sanger died on Tuesday.

For someone like me his name is forever associated with Sanger sequencing - the first and until recently most widely used method of sequencing DNA - finding out the order of nucleotides in genomes that let us understand how they work. Now it has been largely supplanted by Next Generation Sequencing methods that are much faster and have higher throughput but Sanger sequencing is still used by many to sequence small DNA samples (it takes forever to use it for whole genomes). It's till the most accurate method, especially for longer fragments. That was his second Nobel award.

His firs Nobel came from as revolutionary protein sequencing. Back when he started it wasn't sure if the proteins have some definitive composition and when he determined complete amino acid sequence of the two polypeptide chains of bovine insulin he has shown that proteins have a defined chemical composition - an amino acid sequence.

His work changed all our lives - from diabetics who get insulin shots to all the products of genomic studies. To me - he made my field possible. Molecular genetics wouldn't be what it is without him.
ellestra: (tiger)
One of the base facts of biology that prves evolution from common ancestor is the fact that all organisms on Earth share the same genetic code (except for tiny differences in some very old organisms among Archea and things like mitochondria). Codons made of 3 bases correspond to either one of the 21 amino acids used (some amino acids are coded by more then one codon) or a stop sign (stop codons) that truncates protein syntesis. The meanings of those codons is the same in all organisms which is why we can genetically engineer bacteria to produce human insulin by putting insulin gene in it. It's also why viruses can move between species (nature's genetic engineering). One of those stop codons was replaced and recoded in an E. coli strain creating a different genetic code (making aliens). It was change to code for an amino acid that is never used in nature leading way to a designer proteins. This is more radical change then any GMOs because it creates a new lanuage of biology that 7s incompatible with all other life on Earth (it also makes it hard for it survive due to lack of ec8system). Some day it may even mean we'll get to make proteins fom D-amino acids.

Women are already stressed out about aging in our culture of eternal youth cult and obligatory sexiness and then it turns out that women's breasts age faster than the rest of our body. The metylation status of DNA from different tissues in the body can give information about relative age of theose tissues. Researchers checked the changes of methylation with age and compared them to other markers of molecular aging like telomere lenght and then used that to estimate the ages of different tissues. Hearts are about 9 years younger but woman breasts are 2-3 years older. And you thought that the pressure for getting breast plastic surgery was already high.

The last 12 months were hottest on record in Australia. This resulted in massive bush fires that got Sidney covered by gigant smoke cloud. As temperature rises so does droughts and fires prevalence. This is all our fault.

Long time ago when analog, over the air radio and TV were the thing you would scan for the programs and in between hear and/orsee white noise of background radio waves. The empty space between stations was needed so they wouldn't interfere with each other but with the advent of digital broadcasting they became wider than necessary. One proposition to use this free space is to provide wireless Internet and one such project in UK goes on trial.

Wikipedia is crashing on the paid-for 'sockpuppet' entries. Wikipedia doesn't do ads and begs for donation to avoid conflict of interest and being forced to promote sponsors. So I'm not surprised they aren't happy. Even though it was inevitable someone would get this idea and try to profit from it.
ellestra: (tiger)
Nobel Prize in Physiology and Medicine was awarded for cell package delivery system - vesicles. Membranes not only separate cells from outside but also create separate compartments inside the cell - most notably nucleus and mitochondria - but there is also long series of something that looks almost like a tube system. Ribosomes stick to part of it and produce proteins. Those proteins end up inside and can be transported inside but the system is long and twisted. Just like it's faster to take a ferry from Gdańsk to Stockholm then drive all around the Baltic Sea it is faster to send a stuff packaged from one compartment to the other. In a vesicle. That transport is highly regulated and used for many different things. That's how cells absorb the food from outside, how they spit out and absorb hormones and how they transport transmembrane proteins. All the countless ours I spent learning how the phagocytosis and endoplasmic reticulum and Golgi apparatus worked I never thought about people who made all those discoveries. It's funny how at some point things like that become basic knowledge of the subject - something you just know.

Prof James Rothman, from Yale University, found proteins embedded in the vesicles which act as the docking mechanism meaning the cargo is released in the correct location. Prof Randy Schekman, from the University of California at Berkeley, discovered the genes which regulated the transport system in yeast. He found that mutations in three genes resulted in a "situation resembling a poorly planned public transport system". Prof Thomas Sudhof, originally from Germany but now at Stanford University in the US, made breakthroughs in how the transport system works in the brain so that neurotransmitters are released at the precise time.

I was disappointed at the journalist disappointment because this is a very important system in the cell and the basic science Nobels are the ones touching the most important subjects.

Nobel Prize in Physics was awarded to people who theorized existence of Higgs boson - Peter Higgs of the University of Edinburgh, UK, and François Englert of the Free University of Brussels, Belgium, have won for developing the theory of how particles acquire mass. The theory is 50 years old but the experimental confirmation is brand new - not even a year old - so the delay in the announcement wasn't that surprising. Ever since few spectacular mistakes at the beginning Nobel committee has preference for waiting long enough to see that no one disproves it and that multiple sources can repeat the results. Still this was a big thing in physics and a long awaited one. And if they didn't do it now there might've not been another chance. Both laureates are in their 80s and Nobels are not given to dead people. I'm most disappointed in comparisons of the problems of finding Peter Higgs for comment during his vacation with the search for Higgs boson.

The Nobel Prize in Chemistry went to theoretical chemists for devising computer simulations to understand chemical processes. Michael Levitt, a British-US citizen of Stanford University; US-Austrian Martin Karplus of Strasbourg University; and US-Israeli Arieh Warshel of the University of Southern California will share the prize. Modelling molecules is becoming a bigger and bigger thing in drug production where new molecular compounds are first tested for possible uses and molecular interactions before spending money on costly synthesis. It can also help predict protein shape and function which helps to understand how cell processes actually work. Those programs use the equations of quantum physics to simulate reactions as closely to reality as possible. It of course requires vast amounts of computing power to describe every electron and atomic nucleus so these detailed models are limited to small molecules with just a few atoms. To model larger molecules we still need to use classical computer models but they do not include descriptions of molecules' energy states, which is vital for simulating reactions. Still they both allow us to sift faster through the possibilities then any RL experiment and concentrate on most plausible possibilities making discoveries faster and drugs (just a little) cheaper.
ellestra: (sunrise)
Men can have children till the end of their lives. Women limited number of eggs and get menopause somewhere in the middle of theirs. We've been treated to the terror of women biological clock in hundredths of movies and TV shows. You have to get pregnant quickly or all is lost so it's women's main life motivation, right? Well maybe not for long. Researchers have found a way to wake some of the millions of immature eggs that remain, even after a woman has stopped menstruating and produce eggs that are capable of being fertilised. The first test of this technique has resulted in a baby boy, born in December 2012 in Japan. Women only release around 400 mature out of millions that one is born with. Previous experiments shown that there are two pathways that stop eggs from maturing PTEN gene pathway and Hippo pathway(they also suppress cell growth which also stops cells from growing into tumours so they are important). Right now the procedure requires removal of the ovaries to cut the Hippo pathway and then treatment with a PTEN inhibitor. Out of 27 women with premature menopause who went through this procedure three have had their embryos implanted, resulting in one birth and one on-going pregnancy. The third failed to implant. So this is not something you should count on but this is just a beginning.

NewScientist has a big Climate Report collection of articles explaining the latest findings shown on UN's Intergovernmental Panel on Climate Change. It's not a pretty picture - from animals dying due to habitat fragmentation to loss of arctic ice. We may destroy the planet before we agree to admit we do it. Even if you just look at the change of average surface temperatures all over the world and other graphs showing accelerated climate change on Scientific American it's kind of scary. Except for the deniers, of course. I doubt even being flooded wouldn't convince them.

Something that was long suspected has been finally proved - sonars are responsible for whale beachings. The deaths of over 100 melon-headed whales, which stranded on the shores of a lagoon in Northwest Madagascar in 2008, were likely primarily triggered by a form of sonar being deployed by an ExxonMobil survey vessel. This seems especially true for high-frequency sonars like the one used in this case and active sonars navies use. Usually the marine mammals try to escape but it can lead them to get trapped or the sound can damage their inner ears leaving them unable to navigate. In other words there's nothing we couldn't pollute.

Randall Munroe has an asteroid named after him and it's big enough to kill dinosaurs (or all of us). Now I'm jealous.
ellestra: (tiger)
This was taken from lungs of a woman:


She has asthma and her lungs produce white stringy phlegm with a consistency between goat’s cheese and chewing gum. This appears connected to crystalline structures typical of calcium deposits and cells containing lipid particles shown by electron microscopy. This is one of my nightmares as I too had recurrent respiratory infections since childhood and the phlegm produced in my body during the asthma season is so dense I can fully remove it and it sticks on my voice cords and my voice disappears in random moments (if you never experienced pulling phlegm out of your body like a string because it so sticky it never breaks I hope you never will). I keep taking steroids even though they do bad things to my body weight (and beta agonists may quicken the arrival of glaucoma) because they help me breathe. But I none of my skin tests or IgE level measurements has ever given any clue to what I'm allergic too. One doctor mentioned my lungs may just be super sensitive to small particles - so problems during spring and with dust during building and renovation and other things like that.I haven't had any recurring respiratory infections for few years but this part really got me worried:

Treating a presumed but not proven diagnosis can lead to serious side effects aggravating the patient’s symptoms. Both a weight gain of >30 kg and the development of pulmonary tuberculosis is likely to be related to long-term steroid therapy.


And this is how a spiral into hypochondria starts. Dum, dum, dum.
ellestra: (tiger)
Chronic lymphocytic leukemia is most common leukaemia in adults and is incurable. The medicines used right now can only prolong the life (luckily the sickness itself is pretty slow) but not cure the disease. However, Polish scientist Ida Franiak-Pietryga from Łodż's Copernicus Hospital has discovered a substance that specifically targets the sick cells and makes them commit suicide (apoptosis). Dendimers are polymers (like plastic) that have branched, symmetric and spherical structure with a lot of empty space inside and a lot of functional groups on the outside. Due to that structure they are favourite nanotechnology testing material because you can both hide something snide them and stick something to the surface that will allow you to target for specific applications. Dendimers have been known before to be able to attach themselves to and kill cells. The version made by Ida Franiak-Pietryga seem to specifically target leukaemia cells and make them go through the programmed cell death. (in Polish) It still doesn't seem to have made the English language news so all I can give you is link to the original paper and wikipedia explanation of dendimers.

It's been long known naked mole rats don't get cancer despite being extremely long lived for their size but no one knew why. Till now. The substance responsible is called hyaluronan (HMW-HA) and it's a high molecular mass sugar and it’s common in the skin, cartilage, and other connective tissues where it works as a thickening agent. It's produced by the skin cells of naked mole rats in quantities over five times bigger than ours. Its anti-cancer qualities seem to be the result of the way it prevents cells from breaking free and growing into tumours. It may also prevent cells from dividing when they become too crowded (a process called contact inhibition).

Thanks to a donation scientist in Germany were able to make a highly detailed 3D map of the human brain. They put 65-year old woman's brain in wax to make it more stiff so the task of slicing it into 20 micrometres thick sections would be easier. Then they made digital images of the slices at a resolution of 20 micrometres. And finally put more than 7400 sections together which took 1000 hours on a supercomputer. The final resolution of the model is so high, that all the folds are shaped correctly, even if the slice had been cut at an angle. Maps like this will allow us tu understand relations between structure and function better and somday even model the brain (uploading here we come).

As Hank Green song teaches us quarks are fundamental constituents of matter and there are 6 of them - up, down, strange, charm, top, bottom, and they usual create particles usually by combining in threes e.g.: two ups and one down make a proton, while two downs and one up make a neutron but sometimes also in twos - kaons and pions. Although it's not forbidden theoretically no one ever observed particles made from more then 3 quarks. Until scientists at Belle collaboration at the High Energy Accelerator Research Organization (KEK) in Tsukuba, Japan and at the Beijing Electron Positron Collider in China each independently reported evidence for the 4 quark particle called Z_c(3900). There is not enough observations so far to be 100% sure it's 4 quark particle instead of two particles orbiting each other - a hadron molecule that's made of two D-mesons that form a loosely bound state. But that would also be a new form of matter so it's weird no matter what.

I started with patriotic bit and I end with the one that is for my new local affiliation - 3 year old boy hears his father for the first time:
ellestra: (cosima)
I was thinking about writing my thoughts about the first series of Orphan Black as a whole and each of the characters but then a question made me realise there were some more biology to talk about so lets do that first.

First some terminology. Genotype is all your genes. Everything they code no matter if it's ever expressed (used) or if it's important. The whole 3.2 Gb (gigabases - billion bases). However, you need to remember that we humans are diploid organisms. This means that we have 2 copies of each gene (2 alleles). And if they are different we may see only results of one or a mix of those two. I explained a special case of how that works last time when I wrote about X-chromosome and calico cats. They have two alleles - orange and non-orange (black) and we see mix of them depending on which one is inactivated. In peas that have both white and red alleles the result is pink. This visible representation of you genotype is called phenotype. And as I mentioned in previous post phenotype of genetically identical organisms can be pretty different.

We also see it in identical twins as some are more identical then others. Identical twins can have different hights, weights and sometimes even medical conditions (once again more in depth look at that is in previous post). There are mirror twins - they bodies are mirror images of each other from hair parting on opposite sides of their heads to different handedness. And then are things like immune system which is designed to mutate to create all the variations of antigens that are defending us from all the stuff that attacks us. The way this happens through random change means that no two immune systems produce the same antibodies. The closer you are related just gives you the higher similarity. All this means that the phenotype of clones would also differ. And while you age and your cells collect mutations and different epigenetic patterns the phenotypes differ more and more.

Cosima initially doesn't consider any genetic differences despite between the clones. When she asks her labmate to sequence the genes known for being related to respiratory illness she suspects they all have the same susceptibility but it's the environment makes it show up in phenotype. He only sequences tiny part of her and Katja's genomes (4 kb from 3.2 Gb) but they get lucky as they find artificial sequences in that. One of them turns out to be patent notice and the other a barcode unique to each of the clones (except Sarah and Helena who are implied to have the same one).

Is that barcode sequence enough to make them genetically non-identical?

No. I called 4Kb tiny fragment of gemome. That barcode sequence was a tiny fragment of that. It doesn't make Sarah and Helena more alike and others more different.

A lot of our genome is made of non-coding DNA - 98% in fact. Coding DNA are genes - the one that produce proteins and RNA that do all the work in the cells while DNA stays in the library (nucleus). However vast majority of our DNA does not code anything. A lot of it plays important regulatory role but the rest is just there. You could insert stuff in it without changing anything. In fact there is a lot of stuff inserted there. Dead genes (no longer functional), remains of viruses that inserted themselves into our genomes long time ago and never managed to get out and repetitive sequences that can change number of copies (although some of those can lead to serious genetic diseases if it happens in wrong place and in too many copies - Huntington's disease, fragile X syndrome leading to autism). Even if ENCODE is right and 80% of genome has biochemical function there is till plenty of free space.

Especially since the difference between clones is tiny - it's just a few bases (just the barcode that's unique to each one of them) out of 3.2 billion. For all intents and purposes that's no difference at all.

The only way for it to make a difference is if it happened to be inserted in a gene then that gene would be mutated and either inactive or functioning differently. In first case it would be the same for all the clones. In the second there might be a difference since barcode sequences are different so the gene could be malfunctioning differently. However Cosima's labmate says they are no respiratory markers suggesting that all the genes are intact and the artificial sequences he discovered are in non-coding regions. They still can impact the regulation of the gene (how much protein is being made) and that may have dire consequences (COX gene he mentions is part of Electron Transport Chain that is crucial for cell respiration - blocking it is how cyanide kills) but neither he nor Cosima nor Daphne seemed worried so it's nothing obvious.

Bigger differences could be seen if the barcode sequence was in trasposon as transposons are genetic sequences that can jump all over genome. They can cut themselves from one place and insert somewhere else or multiply. They are often leftover of long extinct viruses. If they happen to insert themselves into genes or regulatory elements they can lead to a whole range of of problems depending on where the transposon lands. We all have transposons in our genomes. They usually stay put or even if they jump there is so much of non-coding DNA that they land somewhere relatively safe but they can be responsible for cancer. Since this is happening randomly it means your own cells are not genetically identical but the difference is still not enough to call them someone else's and that's also true for clones. And neither of our scientist seems to spot any tell-tale sequences signalising transposon presence so we can probably assume the artificial sequences are fixed and stable.

Biology is not destiny and genes are not a fixed path. It's more like a general direction and you and the environment you live in makes the path you chose to travel in that direction unique and unrepeatable no matter how close your starting points where.
ellestra: (cosima)
The first season of Orphan Black finished yesterday anlyd it was awesome ride all the way through. Now, I'm more sad I have to wait for more till spring 2014 than I am about waiting for Doctor Who 50th anniversary. I have so many reactions - too many for this post - so biology goes first because priorities.

I was very cautious about this series at the engaging. I wanted to like it but the subject of the show made me anxious. The way that the clones are imagined in a pop culture is to biologists what (I assume) physicist feel about sound in space. Only it's worse because the worst physics mistakes have been (mostly) laughed out of existence. Biology doesn't have as much traction. Things like The Godsend where being cloned makes you evil zombie (or something) and all the cheap sf, pulp-fiction stereotypes that they are identical, faceless copies that think and act the same and not really human reinforced by such popular franchises as Star Wars make cloning the most dreaded subject in fiction as neither of those has anything to do with how it actually works. The misconceptions are so popular and widespread that I spent most of my biology studying years reassuring my family that I'm not cloning people and not planing to and by the time I got to explaining how it's nothing like what they show in movies nobody was listening. So even a mention of a word clone in any movie/tv show makes me cringe in anticipation of pain.

However, the previews and descriptions of Orphan Black implicated that this show will be better at handling the matter but they did it way better then I could ever expect. Someone did their research and/or asked an actual biologist because this series did everything right.

From biological standpoint twins are clones. And clones are identical siblings. They are not copies of the the original. One is not more (or less) real then the other. They don't share a souls (whatever that might be) or even a mind. They are not worth less then other people nor are less real people. The way we make clones from adult animals right now may make them sick but it doesn't make them any less real (just like having progeria or being deaf doesn't makes you less real). We cannot make human clones, yet, but even when we do they wouldn't be the same person as the adult they are genetically identical with. They, every single one of them, would be a different person with their own life experiences and their own personality and memories and life. Just like twins are. Sharing genes is not sharing life. Genes don't code memories. Genes just create a framework of what organism can be - borders made of abilities and possibilities - and then life experiences pick which of them become realised. Differently every time.

I think I repeated that over and over again when explaining why the pop culture take on clones is wrong and now I finally don't have to. I can just tell people to go watch Orphan Black where the clones are all their own people. I was almost squeeing from joy when Sarah said "There is only one of me!" She is not Beth no matter how good she is at impersonating her. She doesn't know police procedures and doesn't behave like Beth. She only gets away with this because it's easier for people to assume Beth is behaving weird because she had nervous breakdown than actually notice they deal with a different person (just going with more likely explanation). But his can also go for so long before inconsistencies build up and everything falls apart. And Kira, Paul and Art eventually all know they are dealing with different people and, thanks to Tatiana Maslany's amazing performance, we feel the same.

And also thanks to the people who design her looks it feels like all her characters look alike but are not completely identical. This is also biological truth. Especially for females, because of the random X chromosome inactivation. In mammals females have one chromosome X more then males so one gets inactivated to equal the number of active genes for both sexes. The pattern of that inactivation is random and differs even between identical twins. And clones. The best examples of this are female cats as there are colour genes encoded on X chromosome - orange and non-orange (black). This is why tortoiseshell cats are (almost) always female and the pattern of black and orange follows the different X chromosome inactivation in different skin cells. How different it can get you can see in tabby and white CC (CarbonCopy of CopyCat) - clone of Rainbow who was calico.

This X inactivation is also true for humans so identical twin girls can be pretty different just because their active X chromosomes may make them different and they can have different genetic disease symptoms (eg. genes for colour blindness and ocular albinism are on X chromosome and so are some that can cause haemophilia). Usually only men show symptoms of those and women are carriers because getting to non-functional copies is very unlikely but if one has a very bad luck at the inactivation lottery the symptoms of the disease can show up in a woman who has a faulty gene on only one chromosome.

There are also other ways that make twins differ. Starting with epigenetics which can activate or deactivate genes differently. Epigenetics is very similar to chromosome inactivation only on smaller scale - just small parts of genome are affected but that may mean genes are functioning differently or with different strength. So this can also mean that they can have different diseases, differ in hight and body looks etc.

Epigenetics in turn can be influenced by environment - from mother hormones in the womb to the food and sun exposure. Environment can also modify things like weight and hight, change a little skin and hair shade and structure, be responsible for need for glasses and teeth braces. In some cases (skin or tissue infection) changes in looks can be pretty drastic. So can be changes in mental health.

Another thing that can be influenced by both environment and epigenetics is brain development and this includes sexual orientation. Both also have influence on such traits like antigen production and fingerprints as both of those things are similar among twins but not identical. The twin fingerprints would still have a lot of similarities they are just not completely identical (just like their immune systems). This is something that once again shows the research that went into the show as they always say similar enough to flag recognition - not identical. I'm not expert on the fingerprint recognition in law enforcement so I don't know how likely it's to flag a twin. I don't know how many same features they have to have to show up on automated search but this might be true and only final precise check by an expert can eliminate twins. Maybe the sensitivity of that search explains why Katja's prints flagged Sarah but Sarah's record didn't flag Beth (as police officer her prints should've been checked).

With so many different mothers and therefore environments that shaped Orphans biological differences between them (from sexual orientation to the respiratory symptoms showing up) could be even greater then what we saw so far. Will all of them get sick? Will they do it at different ages? Will they all have the same body shape? We are after all bound by Tatiana's looks (although maybe we can get different hight and body weight for some new versions next season) but make up and effects can do wonders.

All this shows the attention paid to science. It's almost incredible how it completely discards stereotypes about clones and just follows actual reality of how it would be if they existed (but this is the show where people act more like real people then most of what we see on TV so maybe it isn't that surprising it does the same with science). It's like someone asked a biologist what the clones would actually be liked and listen instead of saying that's not dramatic enough.

All of this makes me think that the purpose Dayad Istitute created the Orphans for is observation of how the environment makes them different. All the test they do and samples they take from the ones under observation. All the monitors to observe the behaviour (and the ones we saw are usually lovers so ones that observe almost every possible aspect of their lives). And this isn't that far out. Some in vitro procedures can result in two identical embryos (I described how we do it on purpose to animal embryos before) and if one of them is frozen and then implanted years later you can even end up with twins that are different age. There are many studies that depend on observing and comparing monozygotic (identical) and dizygotic (fraternal) twins. Including comparisons between ones raised together and apart. Those studies try to find which characteristic are genetic and which are environmentally based. Also most of the animal research is made on mice and rat strains that are artificially made to be genetically identical as it is easier to find the cause of differences if you can repeat the experiment multiple times on identical subjects. If you know that what you started with was identical at the start and you observed everything that happened then finding how they differ after time has passed an what caused those differences can make great discoveries (and a lot of money).

The other thing I realised watching yesterday's episode is that the way that the Orphans seem to be created doesn't seem to involve any original. They seem to have an artificially created sequence (Cosima explicitly mentions Craig Venter's group work on synthetic biology that include making - for now very simple - organisms from scratch) which was then inserted into multiple embryos with appropriate barcode for each try implanted into multiple surrogates and given up for adoption all over the world. So they are all equal. This may also means that they don't really have parents (so Amelia was as close as Sarah will ever get to having a parent even though they were no more related then she and her foster family are). But it also explains the patent.

Living organisms can only be patented if they are significantly different from natural ones. The GMO - crops (e.g. pesticide resistant plants) or laboratory animals carrying specific mutations (mice strains) - can be patented but not the ones that are present in nature (artificial. Although, this law explicitly excludes humans (but not human cells eg. cell lines) - this part might be creative license (the sf part of the show). Then, especially if one - lie Prolethians - doesn't believe clones are human (again not science - pop culture mixed with that weird religious stuff about soul) can lead to legally treating them as property (things).

However, one can patent human genes (if not human organism). This has very real life consequences that just came back to public conciousness due to Angelina Jolie's operation as BRAC1 and BRAC2 genes are owned by Myriad Genetics and only thy can test for mutations and research those genes and their health consequences making it much more expensive for everyone to get tested (there is a lawsuit going on right now that tries to forbid such practices). So Orphans are allowed to live like normal humans but all the knowledge that comes from their lives and their health information belongs not to them but to someone who owns their genome. The law might be against them on that one especially if they are synthetic (and then Dyad makes sure they have all the rights by making them sign the papers - they agreed to it). Although patents have expiration date and, even though I'm not sure how old Orphans are, I think it should've expired (it's usually 20 years).


I love that show shows both that they are all unique human beings they but also makes them struggle with the cultural prejudices about cloning and artificial reproduction even with themselves. I can say that scientifically they are as human as everyone else but it won't change the society reaction (just like the fact that races are not real, biologically, doesn't mean the concept doesn't affect out daily lives) and suspicion and human prejudices that can work against them on many levels - identity problems, social rejection and law status.
ellestra: (telamon)
So I concentrated on body augmentation but other things happened in science recently, too.

We learned last years that dolphins introduce themselves by name (their signature whistle) but it turns out they also call friends and family members by their names (copy their signature whistles) when they look for them. That's makes them the only other animals, other then us, who call each other by names. And they also exhibit almost all our social behaviours - from extremely good to extremely bad - which shows on how fragile foundations our feeling of uniqueness is built (and that you think before you eat someone's mum).

Our whole universe might be even more fragile as scientist who study Higgs boson think that if the the recently discovered Higgs-like particle is really Higgs then its mass would make the universe inherently unstable, like a pencil balanced on its point. The vacuum of space should be most stable at its lowest energy and current Higgs mass calculations indicate that this is not it yet so our space is only temporarily stable and will ultimately collapse. Eventually, a little bubble of an alternate universe will appear somewhere, and it will spread out and destroy us. But some experimental results indicate that there might be more particles so Supersymmetry may save the universe, yet.

Speaking of pens and 3D-prining (I know it seems to pop up everywhere recently) - you can kickstart (and eventually own) a 3D-printing pen. It will use fast solidifying plastic and you will be able to doodle objects that you can then play with. This is like my childhood coming true as one of my favourite Polish children toons was Zaczarowany Ołówek (Enchanted Pencil) - whatever the main hero drew with that pencil became a real 3D-object. I used to wish I could have a pencil like that. Now, I can. I love living in 21st century.
ellestra: (winged)
[livejournal.com profile] jaylake, whose books, you might've read, has cancer. Really bad, aggressive, not-responding to treatment cancer. In last resort they will try whole genome sequencing hoping to find out what kind of mutations are fuelling his cancer and if there is a better treatment associated with that specific types of mutated genes. It still might not work but it is a chance. However, it is also very expensive.

I mostly forget how expensive it still is. I do it everyday (mostly not clinical but research so we are less time oriented but still a lot of it is people and some of that is cancer) and you cannot think of the money involved all the time because it would be too distracting but it is very expensive. We are preparing for new, faster, cheaper technologies but not yet. And time is also crucial here. The whole procedure to prepare the sample, test it and sequence enough to get the whole data. And then waiting for the sequencing to finish and then for data analysis means it also takes time. A lot of time.

I keep wondering whether in his case exome sequencing wouldn't be better than WGS. Exomes are only those parts of genome that actually code protein - without all the spacers and other structural junk. It's much smaller subset of the whole DNA so it would be cheaper (and depending on the method used for sequencing might be also faster) butt there is of course some information lost that way. This is probably way they want everything - no time to redo if the results are inconclusive.

So it will take time and money (and money to buy time and speed things up) there is a foundraiser set up to finance the sequencing. A lot of Jay Lake fellow SF&F writers are donating an "Act of Whimsy" - a thing, a project they will do if certain fundraising goals will be met. It's already over 38K so a lot of "Acts of Whimsy" have been unlocked. It also created a small problem when the donations were submitted to Jay's PayPal account and PayPal promptly froze them suspecting fraud due to sudden influx of money. The thing was quickly resolved due to all those famous (or at least having a lot of followers, including those in tech world) friends who complained all over social media but it was an unwanted delay in a process that was all about speed.

The "Acts of Whimsy" are out there to enjoy and more will be coming and they are awesome. You can still donate to see more of them and help Jay or at least some future scientists and patients who can benefit from the knowledge gained from sequencing his cancer.
ellestra: (Default)
So it looks like there will be no announcement of "for history books" discovery on Mars. No organics, life, aliens or even twinkies. I'm not really disappointed because I didn't expect much. He said they need to confirm the results and they were probably unable to. Happens all the time in science. The mission just got started I'm sure it will find a lot of coll things before it's done.

Cool things like ice on Mercury. Real water ice on the planet so close to the Sun it orbits it in 88 days. The image of scorched small planet is so ingrained I sometimes forget how fast and how cold the parts Sun doesn't reach are and that there must be all the temperatures in between. Thank you Messenger for awesome news.

Even bigger news is the biggest black hole ever discovered. It's in the middle of a very small galaxy and it could shake the foundations of current models of galaxy evolution as its mass is much greater then they predict (17 billion times the mass of the Sun). It also takes much more it's galaxy mass then we've ever seen (14% of the total galaxy mass). Maybe Peter Hamilton was right and someone is powering their paradise.

On the opposite end of scale someone finally took a picture of the DNA. Till now we only new how it looks from secondhand sources (like X-ray crystallography) but now it's the electron microscopy time and the helix is clearly visible in all it's glory.

On even smaller scale there is a new transistor that controls the flow of atoms, rather than electrons creating superconductors out of superfluid atoms, flowing with no friction or physical resistance. So take some very cold superfluid and add some lasers and get you can have a transistor. Not very energy efficient but certainly very cool (like 500 nano-degrees above absolute zero).

And BTW do you remember the Niantic Project I mentioned last week? Well, players are having fun but the really cool thing might come out of all the data Google is able to get through this. Everything points to them using it to set up the Augmented Reality for Google glasses. Part of me feels like this is Google taking last bits of privacy and discovery and just mapping the rea into virtual like in some distopian novel and using us to do it with our own hands (and phones) but I don't even care because players enjoy it and I want AR. This is the future I was promised.

May 2016

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