The DNA Network |
| Busy Busy Busy [The Daily Transcript] Posted: 08 Jun 2008 08:23 PM CDT Well I won't be doing much blogging in the coming weeks. Last Wednesday I found out that I will be giving a talk this Thursday at the University of Toronto. This news came to me while I was smack-dab in the middle of one of these huge experiments. Of course the experiment failed (but I did learn something!) The trip to Maple Leaf land means that I will be missing our upcoming New England RNA Data Club (aka NERD Club). It looks like I'll be landing in Toronto Tuesday night. So Wednesday I'll be reconnecting with my homeland (and practicing my powerpoint presentation). Read the rest of this post... | Read the comments on this post... |
| Existential Moment of Truth [] Posted: 08 Jun 2008 05:16 PM CDT Aminopop editor Thomas Scoville weighs in on Eye On DNA’s question, “What does DNA mean to you?” Quote:
“DNA suggests a moment of truth, historically speaking. Wresting our ongoing genetic definition from the mostly cruel forces of natural selection is going to be a profoundly defining moment. What is human? It's what we say it is — and what we write that it is, when we master the glyphs, grammar and syntax of the genome. It's the ultimate act of existentialism.” (Link) |
| The Platypus: Genetic Mash-Up [] Posted: 08 Jun 2008 04:58 PM CDT
Venemous spines. Eggs. Mammaries. Fur. Duck-bill. It’s an animal in the spirit of our times: Platypus, the Genetic Mash-up. The Medical Research Council Functional Genomics Unit in Oxford and the European Molecular Biology Laboratory’s European Bioinformatics Institute in Cambridge have mapped the platypus genome, finding a wild patchwork of animal classes showing it to be a bizarre mixture of mammal, reptile and bird. |
| Origins of the brain [Think Gene] Posted: 08 Jun 2008 04:19 PM CDT One of the great scientific challenges is to understand the design principles and origins of the human brain. New research has shed light on the evolutionary origins of the brain and how it evolved into the remarkably complex structure found in humans. The research suggests that it is not size alone that gives more brain power, but that, during evolution, increasingly sophisticated molecular processing of nerve impulses allowed development of animals with more complex behaviors. The study shows that two waves of increased sophistication in the structure of nerve junctions could have been the force that allowed complex brains - including our own - to evolve. The big building blocks evolved before big brains. Current thinking suggests that the protein components of nerve connections - called synapses - are similar in most animals from humble worms to humans and that it is increase in the number of synapses in larger animals that allows more sophisticated thought. “Our simple view that ‘more nerves’ is sufficient to explain ‘more brain power’ is simply not supported by our study,” explained Professor Seth Grant, Head of the Genes to Cognition Programme at the Wellcome Trust Sanger Institute and leader of the project. “Although many studies have looked at the number of neurons, none has looked at the molecular composition of neuron connections. We found dramatic differences in the numbers of proteins in the neuron connections between different species”. “We studied around 600 proteins that are found in mammalian synapses and were surprised to find that only 50 percent of these are also found in invertebrate synapses, and about 25 percent are in single-cell animals, which obviously don’t have a brain.” Synapses are the junctions between nerves where electrical signals from one cell are transferred through a series of biochemical switches to the next. However, synapses are not simply soldered joints, but mini-processors that give the nervous systems the property of learning and memory. Remarkably, the study shows that some of the proteins involved in synapse signalling and learning and memory are found in yeast, where they act to respond to signals from their environment, such as stress due to limited food or temperature change. “The set of proteins found in single-cell animals represents the ancient or ‘protosynapse’ involved with simple behaviors,” continues Professor Grant. “This set of proteins was embellished by addition of new proteins with the evolution of invertebrates and vertebrates and this has contributed to the more complex behaviors of these animals. “The number and complexity of proteins in the synapse first exploded when multicellular animals emerged, some billion years ago. A second wave occurred with the appearance of vertebrates, perhaps 500 million years ago” One of the team’s major achievements was to isolate, for the first time, the synapse proteins from brains of flies, which confirmed that invertebrates have a simpler set of proteins than vertebrates. Most important for understanding of human thought, they found the expansion in proteins that occurred in vertebrates provided a pool of proteins that were used for making different parts of the brain into the specialized regions such as cortex, cerebellum and spinal cord. Since the evolution of molecularly complex, ‘big’ synapses occurred before the emergence of large brains, it may be that these molecular evolutionary events were necessary to allow evolution of big brains found in humans, primates and other vertebrates. Behavioral studies in animals in which mutations have disrupted synapse genes support the conclusion that the synapse proteins that evolved in vertebrates give rise to a wider range of behaviors including those involved with the highest mental functions. For example, one of the ‘vertebrate innovation’ genes called SAP102 is necessary for a mouse to use the correct learning strategy when solving mazes, and when this gene is defective in human it results in a form of mental disability. “The molecular evolution of the synapse is like the evolution of computer chips - the increasing complexity has given them more power and those animals with the most powerful chips can do the most,” continues Professor Grant. Simple invertebrate species have a set of simple forms of learning powered by molecularly simple synapses, and the complex mammalian species show a wider range of types of learning powered by molecularly very complex synapses. “It is amazing how a process of Darwinian evolution by tinkering and improvement has generated, from a collection of sensory proteins in yeast, the complex synapse of mammals associated with learning and cognition,” said Dr Richard Emes, Lecturer in Bioinformatics at Keele University, and joint first author on the paper. The new findings will be important in understanding normal functioning of the human brain and will be directly relevant to disease studies. Professor Grant’s team have identified recently evolved genes involved in impaired human cognition and modeled those deficits in the mouse. “This work leads to a new and simple model for understanding the origins and diversity of brains and behavior in all species” says Professor Grant, adding that “we are one step closer to understanding the logic behind the complexity of human brains” Source: Wellcome Trust Sanger Institute Josh says: I can’t say that I’m at all surprised. Higher level organisms began using more complex neurotransmitters, even though these are just simple derivitives of normal metabolic molecules or amino acids. A lot of studies like this seem obvious to me, but I realize that it’s bad to just assume things, and it’s usually always worth conducting the study anyway. You then gain more knowledge about the topic. I’m wondering if their research could be of any help to the Blue Brain Project, which is trying to reverse engineer the mammalian brain by simulating neuronal ion channels. |
| Molecular and Cell Biology Carnival #3: Animations [ScienceRoll] Posted: 08 Jun 2008 12:40 PM CDT It’s my pleasure to host the 3rd edition of the Molecular and Cell Biology Carnival. This is the first time I host a non medicine-related carnival, so I really hope you will like the posts I found. Let’s start with an important article from Bitesize Bio: How to reduce your lab's environmental impact. 12 useful tips including non-mercury thermometers, recycling and many more. This incredible animation, found at The Daily Transcript, should entertain you while reading all the submissions.
Cell: Carl Zimmer at The Loom posted about E. coli Evolution Follow-up and answered some questions from the readers as well. The Seven Stones presented us the E. coli transcriptional network. Ricardo Vidal at My Biotech Life shared a new journal with us that is dedicated to Synthetic Biology. Paras Chopra published a funny letter from Synthia, a new organism in this world. Alex Palazzo at The Daily Transcript continued his series about the Future of Cell Biology- The Sweet Life. Research: First, have you checked whether your profession is included in msnbc’s 10 worst jobs in science list? According to The Biopact Team, researchers present new microbial pathways to bioenergy production. Elaine Warburton at Genetics and Health talked about the connection between nanotechnology and gene p53. SciPhu anaylized an article: Use of polyethylene glycol for drying polyacrylamide gels to avoid cracking. Sandra Porter at Discovering Biology in Digital World liked the flash animations of Sanger DNA Sequencing. Here is another short video about DNA sequencing.:
Medicine: I couldn’ resist the temptation to create such a section. But what else to expect from a medical blogger? Of course, biology has a lot to do with medicine. The Ouroboros team examined the question whether advanced glycation endproducts improve chaperone function in the optic lens. Dr. Chock MD PhD told us some facts about Chocolate and Health. Have you ever wondered what kinds of viruses can be found in human waste? Sandra Porter gives you an answer. And the last article I share with you is from Larry Moran, our favourite professor blogging at Sandwalk, who supposed the launch of this service was inevitable: How to Activate Your Junk DNA!
Many thanks to Steppen Wolf (the skeptical alchemist) for giving me the opportunity to host this carnival. Contact him if you would like to host an edition.         |
| Around the Web - June 6, 2008 [business|bytes|genes|molecules] Posted: 08 Jun 2008 09:13 AM CDT People often ask how FriendFeed, etc have changed my blogging. For the better part, there has been no impact, but collecting links for blogging seems to be getting redundant, cause I keep sharing them on FriendFeed. Not sure what to do at this point. I think the events and multimedia have their value. Anyway, so things are on hiatus while I figure this out. Perhaps a return (and this is very possible) to using the weekends for podcasts/videocasts. In the meantime, here is where you go to find them links FriendFeed … and last but not the least, and no least cause I use it very differently from the others, my Tumblelog |
| 23andMe and moderate risks [Mailund on the Internet] Posted: 08 Jun 2008 01:38 AM CDT At Think Gene, Andrew Yates has a review of 23andMe. Mainly about the web interface — that does look cool — but then he concludes:
The sad fact is that, for common SNPs, all risks we know of are small to moderate. If we knew how they interacted, maybe we could detect higher risks, but right now we only see small increases in risk in the SNPs we know about. If you expect more, you will be disappointed indeed. I think personal genomics is pretty cool, but I doubt it has any clinical relevance at this point. I could be wrong, of couse, but that is where I would place my bet. |
| Andrew’s Review of his 23andMe Service [Think Gene] Posted: 07 Jun 2008 11:00 PM CDT Previous: Andrew’s 23andMe kit The Good
23andMe’s excellent trial user account is a manifestation of their excellent user interface design. The graphics are subdued and functional; obviously 23andMe web designers have been making websites long enough not to be impressed with the latest web bling. Instead, what they have created is a clean, easy to navigate, easy to use site out of a tangled mess of complex data and information. Congratulations to the 23andMe web team; you deserve it. Given that a trial account is free to the public, you have created the single most public-accessible repository of genetic information in the world. My single complaint is that some traits unpredictably use an Odds Calculator and others use a “What It Means” table. The Lame I don’t have any family or friends on the system, so both the “family & friends” and the “my ancestors” sections were useless to me. OK, so I’m white and European. I knew that already. The Disappointing Of all the 70 possible traits described by the 23andMe test, no trait reported anything useful except perhaps a moderate (almost 30%) risk of rheumatoid arthritis. Even more disappointing is that despite claims in the press of joining some elite genetic social club, I have yet to be invited to any parties… or even receive an email written in a festive tone. Come on, 23andMe, that’s not cool. Think Gene gets more traffic than you do, so maybe we can be friends after all? |
| Isn't The Great Filter something in the Whatman catalog? [Omics! Omics!] Posted: 07 Jun 2008 09:56 PM CDT Twice in the last week the Globe has run pieces on a concept called 'The Great Filter', once on the Op-Ed page and now in the Star Watch astronomy column. I've read both, and the pseudo-statistical thinking in them just irks me. The headline on the star watch column suggests the hubris that is perhaps what is goading me: "Why a microbe on Mars would change humanity's future". I'd completely agree that discovering microbial life on Mars would be exciting, but where it goes from there is bizarre. The gist of the argument can be found in this quote If life arose independently twice in just one solar system, it would mean that the life formation process is easy and common. Life would be abundant everywhere. Most starts have planets, os the entire universe would be teeming with living things.. Given that we haven't yet found signs of other advanced life (or any life) elsewhere
Okay, just where to start. First, the current Mars mission finding life on Mars is a far cry from finding that life arose independently on Mars. We know that rocks make the transit occasionally, and while we think we sterilized all the probes, the possibility that any life form found really shares a common heritage must first be ruled out. Gary Ruvkun has suggested an experiment for a future probe to look for & sequence ribosomal RNA (if I remember correctly); that would be an appropriate follow-up. There's also the problem of an N of one: Mars is one planet. Maybe you count an N of 2 with Earth as the second case, though since you're trying to predict on it that's a case of training on your test set. Mars is hardly an independent sample; the same solar system, which may or may not have some unusual properties. But perhaps more irksome is conflating the reasonable idea that there are difficult barriers against spacefaring species to arise with the rather silly one that there is a single "Great Filter". Mars is a particularly poor example, as we would have a good guess what the filter is there: the planet quit being a nice place to live. How improbable is life? How often do planets get life but it stays unicellular? How often multicellular but never ambulatory, sentient beings? How often do those sentient beings come up with some way to prevent travel to the stars -- a religion that forbids it, self-extermination (which our species has toyed with). Perhaps some inhabited planets have a super Van Allen belt which dissuaded their residents from becoming star travelers. Perhaps there are intelligent cultures far away -- but with a timing such that their signals can't yet reach us. The fact is, any estimates of the probability of any one of these (or anything else you can imagine) are nothing but personal priors, wild guesses without much basis in fact. Feel free to make them, but spare us the headlines about predicting doom and gloom. |
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