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Ego sum Daniel
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- August 27, 2009
- 08:10 AM
- 1,797 views
Arctic root revisited
by Daniel in Ego sum Daniel
This post is slightly delayed since, you know, stuff gets in the way. But better late than never. A comment on my post "lack of evidence for arctic root "natural medicine" raised a few points that I think are worthy of delving into. I wrote that post quite hastily with the only intention of just mentioning the review by Blomkvist, Taube and Larhammar published in Planta Medica, so it also gives me the opportunity to revisit the subject more in depth.Firstly, let's state the facts as presented by the comprehensive scientific review of the most recent medical studies of arctic root/roseroot published by Blomkvist et. al. Six of the seven recent (since 2000) studies that supposedly showed an effect of arctic root/roseroot had significant flaws, including irrelevant comparisons, inappropriate statistical methods, exaggerated conclusions, and mistakes in the presentation of the data. These mistakes go beyond simple holes in the statistics, they are of embarrassingly poor scientific quality. Some of the problems are quite extraordinary. For instance, Spasov et al. based their final conclusion on a follow-up study that was not described in their article and remains unpublished. Darbinyan et al. claimed to have found a significant improvement over placebo despite contradictory results that they explained away with an unfounded assumption. The second study by Darbinyan et al. used irrelevant tests and an inappropriate statistical comparison. Bystritsky et al. and Fintelman and Gruenwald claim to have observed an effect but did not use a placebo control. Shevtsov et al. is riddled with misprints and mix-ups which make it difficult for the reader to interpret the text and understand the procedure. Also, the use of pulse pressure as a measure for physical fitness is incorrect, and the levels of statistical significance presented in the study appear unreasonably high.They also reviewed four studies (and two reviews) that had not found any effects of arctic root/roseroot in the same critical way and found no errors, but commented that one of the studies had used a small number of test subjects making it of questionable value.The Swedish Herbal Institute (SHI henceforth), makers and marketers of arctic root/roseroot preparations, were involved in four of the six flawed studies. Spasov et al. published in 2000; two studies by Darbinyan et al. published in 2000 and 2003; and Shevtsov et al. published in 2003. As exposed in the op-ed in Dagens Nyheter and summarized in my previous post, there were suspicious circumstances surrounding the publication of two of these articles, both co-authored by Georg Wikman of SHI. These circumstances certainly cast a shadow of doubt over the company as a serious research institution. It should be enough to make any reasonably skeptical person realize that there were serious faults committed in both the scientific and editorial processes.The question is then: How much scrutiny is reasonable? Shouldn't the consumers be allowed to decide for themselves what works for them? Why attack good people and companies that just want to provide people with a product they want? The first point raised in the comment to my previous post was that small companies, such as the SHI don't have the resources available to big pharmaceutical corporations. They are simply doing the best they can with what they have to discover and market the benefits of natural products. Furthermore they should be commended for their efforts and innovation and for having the guts to invest in this research and for giving something back even though they don't have to. The second point is that by referring to the name of this particular company, Swedish Herbal Institute, as deceptive I'm doing the company wrong and hurting the nice folks there. I really find little merit in SHI's supposed "efforts" to do "research". It's pretty clear to anyone that they have not gone through any sort of scientifically satisfying process in generating or publishing their data, despite the ridiculous boasts on their website. I fail to see how their resources (or lack thereof) or their good will has anything to do with their adherence to proper scientific proceedings. Should those companies that can't afford the proper scientific procedures simply be exempt from them? As if it were optional. And why should they be exempt from critical and scientific scrutiny of their work simply because they are nice caring people who provide a service some people want? As a minimum, they should not be permitted to promote and market their product with statements such as "clinically proven to enhance energy and improve mental clarity during stressful periods of work or studies" or "proven efficacy in clinical studies published in international scientific journals", which are clear exaggerations of the already unfounded scientific claims. Both statements appear prominently on SHI's website, as exemplified in the image below, and on many national ads. Currently the Swedish Medical Products Agency lists this arctic root preparation as a so called "traditional herbal medicinal product" (link), meaning that it has been tested for safety but has a very limited scientific foundation, its indications being based only on traditional use for longer than 30 years. This stands in contrast to the claims presented in the marketing of the product. Ref: www.shi.seEven if done in good faith, this can only be qualified as deception. Especially now that the scientific faults of the studies have been exposed. The fact that SHI has a commercial interest in the product and continue to promote is under false scientific claims just gives anyone the more reason to be skeptical about their intentions. As for the second point, the term "institute" is not protected in Sweden, but it would be naive of anyone to deny that both the words "Swedish" and "institute" are sensitive issue when it comes to the naming of companies. A parallel can be drawn to the UK where "British", "English", "Scottish" et.c. and "institute" are protected and are clearly found to "imply national or international pre-eminence" and require the support of representative and independent bodies before they can be approved in a company name (reference).The name "Swedish Herbal Institute", or "Örtmedicinska Institutet" in Swedish, definitely suggests an official level of prominence that the company doesn't have and is therefore misleading. It deceptively mirrors the names given to national institutes, governing agencies and representative bodies such as Smittskyddsinstitutet (Swedish Institute for Infectious Disease Control), Konjunkturinstitutet (Swedish National Institute of Economic Research), Folkhälsoinstitutet (Swedish National Institute of Public Health) and others. They are welcome to continue providing those that feel arctic root works for them with their product, but to do so under the false pretenses that the product has a confirmed clinical effect or that it has gone through the correct scientific testing of the purported effects in the first place is simply unacceptable and worthy of criticism. The fact that the criticism may hurt the company or the people involved in it is irrelevant. In fact, they should welcome the opportunity to defend their statements in the leading morning newspaper of the country and one of the prominent journals in their field, where the criticism has been presented. So far it's been very silent though.Blomkvist, J., Taube, A., & Larhammar, D. (2009). Perspective on Roseroot Studies Planta Medica DOI: 10.1055/s-0029-1185720Swedish blog tags: Pseudovetenskap, Naturmedicin, RosenrotTechnorati tags: Pseudoscience, Natural medicine, ... Read more »
Blomkvist, J., Taube, A., & Larhammar, D. (2009) Perspective on Roseroot Studies . Planta Medica. DOI: 10.1055/s-0029-1185720
- January 24, 2008
- 12:00 AM
- 913 views
Brainbow
by Daniel in Ego sum Daniel
http://olympusbioscapes.com/gallery/2007/index.htmlBeautiful isn't it? This award winning picture shows the brain stem of a transgenic mouse that has been modified using an exciting new technique called Brainbow. The mouse has been modified to express 4 different fluorescent proteins randomly in different neurons. Much like pixels make many different colors possible on your screen, the different random combinations of green, red, cyan and orange fluorescent proteins make it possible to color individual neurons in nearly 100 different hues. You never know from th... Read more »
Jean Livet, Tamily Weissman, Hyuno Kang, Ryan Draft, Ju Lu, Robyn Bennis, Joshua Sanes, & Jeff Lichtman. (2007) Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature, 450(7166), 56-62. DOI: 10.1038/nature06293
- May 13, 2009
- 09:37 AM
- 782 views
Dancing parrots and musical minds
by Daniel in Ego sum Daniel
Look at these videos below. They show sulphur-crested cockatoo Snowball apparently dancing along to a song, synchronizing his movements to the beat and adapting when the tempo changes, something that does not form part of these birds’ natural behaviors. This is no small feat or mere circus trick. Beat perception and synchronization, as it's called, involves not only perceiving the pattern of the rhythm but also coordinating the movements in anticipation of every beat. These are really sophisticated cognitive processes; so sophisticated they were long considered to be exclusive to humans. Not even chimpanzees, our closest extant relatives, are able to keep the beat to an external auditory rhythm. Snowball was brought to my attention by friend and musician Christopher who after reading this report ("At least birds can dance") on the science pages of leading Swedish morning newspaper Dagens Nyheter, declared bluntly that his view of the world had been shattered. To him it was clear that music had been demoted to an inferior position below linguistic abilities. The article declares that "the capacity of perceiving music - even in humans - is an evolutionary by-product that tagged along when we developed the ability to speak and communicate with each other". It’s a very sweeping statement, but it raises some interesting questions.The report in Dagens Nyheter refers to two freshly published articles in the journal Current Biology. In two independent studies Snowball and African grey parrot celebrity Alex were tested to verify if they actually have the ability to move synchronously to an external auditory beat or if they simply appear to be synchronous by chance occurrence or maybe even just mimic the movements of their masters. Hilariously, the researchers were completely unaware that birds could have this ability until a YouTube video of Snowball dancing went viral and eventually came their way. It turns out that yes; these birds are actually able to keep the rhythm. This is the first time it's been shown in a non-human animal. You can see the statistics represented on the figure below. 0° indicates perfect alignment to the beat and Snowball's average is indicated by the arrow.Ref: A. Patel et. al. (see reference below)So Snowball's head bobs did align with the beats pretty well, but not perfectly. As you can see in both videos his periods of synchronicity are interspersed with periods that are more or less off. The authors of the study argue that this could mirror how small children synchronize to music. As demonstrated in the second video, Snowball could also adapt his movements to changes in the tempo, another key feature of beat perception and synchronization. Parrots, like us, are vocal learners; our speech is not innate but learned by mimicking other individuals, often parents or close relatives. The circuits in the brain that underlie vocal learning, which interconnect the auditory system with systems for initiation and execution of movements, overlap with those involved in beat perception and synchronization. So it’s likely that the ability to perceive and synchronize beats, an integral part of our ability to perceive and practice music, is a product of the same neural foundations that gave us language and speech abilities. It seems like some abilities, however important we may consider them, evolved as secondary effects or by-products to other more clearly beneficial cognitive abilities - as evidenced by the fact that parrots exhibit beat perception and synchronization even though they clearly have no use for this curious behavior in their natural environments.However, it’s important to remember that musical ability is not just one thing; it’s grounded in several interacting phenomena with different neural bases. So claiming that our capacity of perceiving music as a whole is a by-product of our linguistic abilities would not be right. The ability to perceive rhythm and coordinate movements to an external beat is an integral part of our musical behaviors, but there are other components as well - the perception of pitch for instance, and the ability to cooperate and create music as a group.So, is our pervasive musicality just a happy accident, or did evolution shape our minds to be musical? Well, until an aspect of musicality is discovered to be innate, with an obvious adaptive advantage of its own, the question remains open. The results generated from observing Snowball and his dancing conspecific highlight the likelihood that individual aspects of musicality could be by-products of other cognitive abilities. This is not surprising considering that this is how evolution works; it builds and expands upon already existing structures and features to generate new ones. We shouldn't give terms like "by-product" unnecessary attention. A more interesting question to ask is why we find musical expression so important and rewarding and why it’s so deeply embedded in the architecture of our minds. That’s when we start discussing the true evolutionary value of musicality. Swedish blog tags: Vetenskap, Biologi, Neurovetenskap, Språk, Musikalitet, Dans, KakaduaTechnorati tags: Science, Biology, Neuroscience, Language, Musicality, Dance, Cockatoo,Patel, A., Iversen, J., Bregman, M., & Schulz, I. (2009). Experimental Evidence for Synchronization to a Musical Beat in a Nonhuman Animal Current Biology DOI: 10.1016/j.cub.2009.03.038Schachner, A., Brady, T., Pepperberg, I., & Hauser, M. (2009). Spontaneous Motor Entrainment to Music in Multiple Vocal Mimicking Species Current Biology DOI: 10.1016/j.cub.2009.03.061... Read more »
Patel, A., Iversen, J., Bregman, M., & Schulz, I. (2009) Experimental Evidence for Synchronization to a Musical Beat in a Nonhuman Animal. Current Biology. DOI: 10.1016/j.cub.2009.03.038
Schachner, A., Brady, T., Pepperberg, I., & Hauser, M. (2009) Spontaneous Motor Entrainment to Music in Multiple Vocal Mimicking Species. Current Biology. DOI: 10.1016/j.cub.2009.03.061
Patel, A. (2006) Musical Rhythm, Linguistic Rhythm, and Human Evolution. Music Perception, 24(1), 99-104.
- October 5, 2009
- 04:21 AM
- 759 views
Anchiornis
by Daniel in Ego sum Daniel
Who wouldn't be completely smitten with this lovely little critter!The latest issue of Nature has published the description of what is billed as the oldest feathered dinosaur, Anchiornis huxleyi. It's adorable! Read more here and here. It's not surprising anymore to find dinosaurs with feathers, as a matter of fact there are several small toy models of feathered dinosaurs on my desk right now looking up at me so they've started to find their way into popular culture. What makes Anchiornis so striking is that both the sediments in which it was found and its characteristics place it at the very base of the origin of birds from small feathered dinosaurs in the late Jurassic, before the oldest known bird, Archaeopteryx. It provides evidence of bird-like features in a time before there were birds. All other feathered dinosaur fossils that have been found have been dated to a later time. There are of course many more interesting details surrounding this finding, but I'll just refer you to the far more knowledgeable articles I linked to above. I just wanted to get something down because this is exactly the kind of thing that gets my imagination going and really takes me back to when I was first "bitten" by dinosaurs when I was seven or eight years old. I can only imagine what I must have thought or felt back then if someone had told that not only had there been small, feathered, four-winged (!) dinosaurs hopping and flapping around on earth, but that all birds were actually living breathing dinosaurs; great, great, great, grand-cousins of Velociraptor or T. rex. I still can't walk past the thrushes and blackbirds that skittishly and vigilantly peck for earth worms out on the yard without smiling to myself imagining a much, much older, but maybe not too dissimilar scenario in the Mesozoic. Hu, D., Hou, L., Zhang, L., & Xu, X. (2009). A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus Nature, 461 (7264), 640-643 DOI: 10.1038/nature08322Swedish blog tags: Dinosaurier, Paleontologi, VetenskapTechnorati tags: Dinosaurs, Paleontology, Anchiornis, Science
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Hu, D., Hou, L., Zhang, L., & Xu, X. (2009) A pre-Archaeopteryx troodontid theropod from China with long feathers on the metatarsus. Nature, 461(7264), 640-643. DOI: 10.1038/nature08322
- May 7, 2009
- 10:17 AM
- 748 views
Religious belief in the brain
by Daniel in Ego sum Daniel
I've often wondered what's going on in the religious brain that is so different from what's going on in mine. How can religious people so determinedly "get it" while I just as determinedly don't. Turns out that, in a sense, not that much is different. Religious belief works through brain networks that have regular non-religious functions, suggesting that religion is nothing but a secondary effect of regular cognitive processes. A study published in PNAS last week (ahead of print) set out to examine which psychological "dimensions" make up religious belief and how the brain processes them, largely through the use of functional magnetic resonance imaging, fMRI - a technique that allows researchers to get images of brain activity in awake test subjects performing different tasks. In this case the task was agreeing or disagreeing with statements such as "God is removed from the world", God is punishing", "God is forgiving", "A source of creation exists", "Religion provides moral guiding" and so on. Some interesting conclusions:The practice of religious belief involves the assessment of god's perceived involvement in the world and god's perceived emotion. So when we ponder god, we use the same brain networks that are used for understanding the intent of people around us, understanding their emotional state, predicting their actions and generating an appropriate emotional response to give back. This is a central mechanism behind our social interactions. This study demonstrates that we think of gods just as we think of anyone around us. There are no particular parts of the brain that are dedicated explicitly to understanding god, instead our brains try to "read" god just as we read the people we interact with. It also seems like the reason some people adopt religious beliefs while other don't is largely emotional, with the effect being larger for those who are believers. When religious test subjects were asked to actively deny a series of religious statements they showed much larger involvement of brain networks involved in the communication between emotions and cognitive processes than non-religious test subjects. You can see these brain regions in the lower row of the figure below. This finding will be familiar to any non-believers who have discussed religion with believer. Their final arguments are often emotional and not logical, they "just know" and they feel negative emotions when considering the non-existence of god. Ref: D. Kapogiannis et. al. (see reference below)I'll take the opportunity to recommend the blog where I first found this study: Epiphenom. It's updated frequently with a lot of very nice information from studies on the neuroscience and psychology behind religious belief. You can read more there. But while the author of that blog states that this study doesn't do anything to prove that religious belief is a by-product of evolution, I see that it absolutely does. The authors even conclude with:The evolution of these networks was likely driven by their primary roles in social cognition, language, and logical reasoning. Religious cognition likely emerged as a unique combination of these several evolutionarily important cognitive processes.To me it's pretty clear that any supernatural belief is an "overshoot" of mental capacities that we use for other purposes, that we relate to supernatural entities just as we relate to those entities we interact with. Whether this is adaptive or not, whether it's been to our advantage or not, is another question altogether. I'm inclined to believe that given the complexity of the brain and the complexity of phenomena it can generate, it's unlikely that all of them, at any point in evolution, are the result of adaptation. The brain simply does too much. I'm open to the thought that cultural phenomena could have "abducted" some of our cognitive abilities more or less "by accident" to generate some of the more colorful phenomena of our cognition and behavior.Kapogiannis, D., Barbey, A., Su, M., Zamboni, G., Krueger, F., & Grafman, J. (2009). Cognitive and neural foundations of religious belief Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811717106Swedish blog tags: Vetenskap, Biologi, Neurovetenskap, Hjärnan, ReligionTechnorati tags: Science, Biology, Neuroscience, Brain, Religion... Read more »
Kapogiannis, D., Barbey, A., Su, M., Zamboni, G., Krueger, F., & Grafman, J. (2009) Cognitive and neural foundations of religious belief. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0811717106
- March 11, 2010
- 05:34 AM
- 692 views
"Why do we believe", and are atheists really more intelligent?
by Daniel in Ego sum Daniel
ResearchBlogging.org editor Dave Munger has written an article for SEED magazine entitled "Why do we believe". The article summarizes recent blog entries regarding studies on the origins of religiosity. It's really worth reading to get a good overview of the subject, and what do you know he links my entry on god's will and beliefs in it.
Among the studies that are mentioned is a controversial study entitled "Why Liberals and Atheists Are More Intelligent" (link at the end of this post).
Medical writer Tom Rees devotes his blog Epiphenom to the scientific study of religion. Last week he examined a study on the relationship between intelligence and religious belief. Published in Social Psychology Quarterly, this study by Satoshi Kanazawa replicated the results of several earlier studies in showing that strong religious belief was correlated with lower intelligence. In this case, adolescents who scored higher on intelligence tests were less likely to be religious as adults.
But Rees says Kanazawa’s study goes beyond those earlier studies to arrive at a potential explanation of why less-intelligent people are more religious: Intelligence evolved in order for people to adapt to novel situations.
You should go over to Epiphenom to read a summary of the study as well as my commentary on it, posted as a blog comment. In summary: I don't think it's very good. Kanazawa's evolutionary argument is completely based on some pretty wild conjectures and lacks any sort of empiric support. His argument is at most "sorta reasonable", but we must do better than that surely. For us real evolutionary researchers that have to spend considerable time and effort gathering a solid line of evidence, this sort of jumping to conclusions can be a tad annoying.
Also, let's remember what kind of forces we're dealing with here, how evolution through natural selection actually acts and what it acts on. Even if we assume first, that intelligence tests do measure some sort of good approximation of intelligence, and second, that results gathered today actually reflect a past situation; what difference do a "good few" average points make for survival? Any conclusions made from the correlation between higher intelligence, as measured by intelligence tests, and atheism are only significant within a larger evolutionary and functional neurobiological context. So take claims that atheists are more intelligent (on average) with a considerable pinch of salt.
Read more on the subject on Epiphenom, here and here.
Kanazawa, S. (2010). Why Liberals and Atheists Are More Intelligent Social Psychology Quarterly DOI: 10.1177/0190272510361602
Swedish blog tags: Vetenskap, Biologi, Neurovetenskap, Hjärnan, Religion
Technorati tags: Science, Biology, Neuroscience, Brain, Religion
... Read more »
Kanazawa, S. (2010) Why Liberals and Atheists Are More Intelligent. Social Psychology Quarterly. DOI: 10.1177/0190272510361602
- August 12, 2008
- 03:58 PM
- 672 views
Genome Biology on race
by Daniel in Ego sum Daniel
The concept of race is something that's often held against biology and evolutionary biology in particular. Genuine concerns based on the use of science (or pseudoscience) in the past to promote racism are mixed with misinterpretations of evolutionary theory to produce a divide between the public and scientific conceptions of race. Deluded creationists and opponents of evolution in particular like to play up and expand this divide by claiming that modern evolutionary theory negates the idea that all humans have equal worth; promoting the ridiculous misconception that evolution reduces us to simple pawns in the "survival of the fittest" and therefore justifies racism, discrimination and genocide.It's welcome then that multidisciplinary group of scientists from Stanford University has put together an open letter in the latest issue of Genome Biology posing 10 statements that very clearly lay down what's what when discussing race in terms of biology, evolution, genetics, medical research and science in general. It's really worth reading all of it, but there are some points worth highlighting: We believe that there is no scientific basis for any claim that the pattern of human genetic variation supports hierarchically organized categories of race and ethnicity.We recognize that individuals of two different geographically defined human populations are more likely to differ at any given site in the genome than are two individuals of the same geographically defined population.We recognize that racial and ethnic categories are created and maintained within sociopolitical contexts and have shifted in meaning over time.We caution against making the naive leap to a genetic explanation for group differences in complex traits, especially for human behavioral traits such as IQ scores, tendency towards violence, and degree of athleticism.If we only could get this through to some thick skulls out there, we'd all be better off. Lee, S., Mountain, J., Koenig, B., Altman, R., Brown, M., Camarillo, A., Cavalli-Sforza, L., Cho, M., Eberhardt, J., Feldman, M., Ford, R., Greely, H., King, R., Markus, H., Satz, D., Snipp, M., Steele, C., Underhill, P. (2008). The ethics of characterizing difference: guiding principles on using racial categories in human genetics. Genome Biology, 9(7), 404. DOI: 10.1186/gb-2008-9-7-404Swedish blog tags: Vetenskap, Biologi, RacismTechnorati tags: Science, Biology, Race, Racism... Read more »
Sandra Lee, Joanna Mountain, Barbara Koenig, Russ Altman, Melissa Brown, Albert Camarillo, Luca Cavalli-Sforza, Mildred Cho, Jennifer Eberhardt, Marcus Feldman.... (2008) The ethics of characterizing difference: guiding principles on using racial categories in human genetics. Genome Biology, 9(7), 404. DOI: 10.1186/gb-2008-9-7-404
- July 31, 2008
- 12:00 AM
- 658 views
"New life" pt. 2 and the minimal genome
by Daniel in Ego sum Daniel
In my last post I discussed why "new" or "man-made" life wouldn't really be all that new and I ended with the suggestion that the road towards making "new" synthetic life might be a goal all in itself. I would like to elaborate a little bit on that and then write something about why Mycoplasma genitalium is so interesting in this respect.The end of creating "synthetic organisms" (a term used loosely) would be something like "engineered" bacteria that would produce specific substances or maybe even catalyze particularly interesting biochemical reactions. This is not that different from what we're already capable of doing, granted it would be in a larger scale. Putting synthesized DNA, especially designed for a purpose, into living cells and having them express that DNA is common practice in molecular biology, even though it has its limitations. You can buy the cells from catalogs and the whole process is carried out with ready-made kits by just following the instructions in the box. The strength of producing "synthetic organisms" would be that you could create entire systems and not just get the bacterium to produce one or a few substances. You could design the biochemical cellular environment of that organism on a larger scale and gear it towards one preset goal. This is because theoretically you could control every aspect of that organism's genome: not only everything that the cell produces but also how it regulates itself. But the key thing to look out for here is "every aspect". We are still far away from having a complete understanding of how genomes are made up. So a scenario where we have absolute control of an organism's biochemical processes seems far ahead in the future - another reason why the headlines of "new" or "man-made" life are exaggerations - but getting there we will undoubtedly have to learn more about how evolution has built genomes and what exactly is needed to constitute a functioning genome. A very exciting prospect. It's in this regard that Mycoplasma genitalium is important. It has the smallest known genome of any self-replicating organism and it's one of the simplest free-living bacteria there are. It only has 482 protein-coding genes, compared to us humans' approx. 20,000 (at the last count). In 1995 it became the second genome to be sequenced for this reason and no doubt this is what makes it such a good candidate to be the stepping stone towards the creation of a "synthetic" organism. By looking at Mycoplasma we can deduce what the minimal requirements are for a genome to work: how many genes are necessary for sustaining life?At the last count in Mycoplasma genitalium from 2006, 387 out of 482 protein-coding genes and 43 structural RNA genes are essential for the growth of this bacterium. This was deduced by mutating gene after gene, making them useless one after the other, and seeing whether or not the mutant bacteria could live and grow. The real interesting number though, is 110. 110 of the 387 essential genes still have unknown function. The genes have been identified in the DNA, but it's still unknown what they do or what hypothetical proteins are produced from them.So we're not yet in a time where we know every aspect of what an organism does, not even one of the simplest ones, and we're not yet in a time where we can design an entire viable genome in our interest and thus control every aspect of an organisms biochemical processes, or in other words, "play god". If or when that day comes, there's no doubt that many exciting and useful applications will be available to us. But let's not forget that during the process we will have acquired a wealth of knowledge about ourselves and indeed life itself that will be difficult to overestimate. Then the answer to the question whether or not we should "create life" (again, using the term very loosely) just because we can, gains a whole new dimension. Glass, J.I. (2006). Essential genes of a minimal bacterium. Proceedings of the National Academy of Sciences, 103(2), 425-430. DOI: 10.1073/pnas.0510013103Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A., Smith, H.O. (2008). Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science DOI: 10.1126/science.1151721Swedish blog tags: Vetenskap, BiologiTechnorati tags: Science, Biology, Genomics, Venter... Read more »
J Glass. (2006) Essential genes of a minimal bacterium. Proceedings of the National Academy of Sciences, 103(2), 425-430. DOI: 10.1073/pnas.0510013103
D Gibson, G A Benders, C Andrews-Pfannkoch, E A Denisova, H Baden-Tillson, J Zaveri, T B Stockwell, A Brownley, D W Thomas, M A Algire.... (2008) Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science. DOI: 10.1126/science.1151721
- June 3, 2011
- 09:38 AM
- 658 views
Turn off the lights and let melatonin run free
by Daniel in Ego sum Daniel
>> I started the following post about melatonin sometime in March to coincide with my lecture on biological rhythms on our undergrad neurobiology course. But I got really busy and then really sick so I never actually finished it. Here it is then at last.
An all too common sight, at least at my place. This is my Mac glaring. But how is our exposure to low-intensity artificial light before bedtime affecting our sleep cycle?
Twice every year I lecture to undergraduate students in biology and biomedicine about biological rhythms, specifically about circadian rhythms - how the brain regulates your daily cycle of sleep and wakefulness. In this process the small suprachiasmatic nuclei (SCN henceforth) in your hypothalamus and the hormone melatonin, secreted from your pineal gland, play very important roles. The SCN is the "internal clock" of your brain and receives light input from the eyes in order to "reset the clock" every morning, signaling that a new day has started. So daylight itself serves as a signal for the brain that it's daytime and we need to be awake and alert, as far as possible.
One of the things I tell my students that usually raises some eyebrows is that even quite low-intensity light, comparable to the illuminance from a computer or television screen, as seen above, can affect the brain and shift the circadian rhythm significantly. This knowledge goes back to experiments carried out in the mid 90's and raises questions as to how artificial light, such an obvious and constant component of our environment, is affecting our day-night cycle.
In a recently published article in the Journal of Clinical Endocrinology (reference 1 below) a team of researchers has shown indirectly that it's the interplay between the SCN and melatonin secretion, so essential to the regulation of nighttime behaviors, that is affected by the artificial light in our environment.
Continue after the jump »
... Read more »
Hardeland, R., Cardinali, D., Srinivasan, V., Spence, D., Brown, G., & Pandi-Perumal, S. (2011) Melatonin—A pleiotropic, orchestrating regulator molecule. Progress in Neurobiology, 93(3), 350-384. DOI: 10.1016/j.pneurobio.2010.12.004
Gooley, J., Chamberlain, K., Smith, K., Khalsa, S., Rajaratnam, S., Van Reen, E., Zeitzer, J., Czeisler, C., & Lockley, S. (2011) Exposure to Room Light before Bedtime Suppresses Melatonin Onset and Shortens Melatonin Duration in Humans. Journal of Clinical Endocrinology , 96(3). DOI: 10.1210/jc.2010-2098
Boivin, D., Duffy, J., Kronauer, R., & Czeisler, C. (1996) Dose-response relationships for resetting of human circadian clock by light. Nature, 379(6565), 540-542. DOI: 10.1038/379540a0
- July 31, 2008
- 12:00 AM
- 587 views
"New life"
by Daniel in Ego sum Daniel
There's been a lot of interest in the media concerning the results published by the J. Craig Venter institute last week in Science - the synthesis of a completely artificial genome, or rather, the synthesis of a down-sized replica of the genome of the bacterium Mycoplasma genitalium. The words "playing god", "man-made life" and "building new life from scratch" have been thrown around, unfortunately; not only because it makes synthetic biology more controversial than it needs to be, but because in essence they're wrong. Carl Zimmer has written two excellent pieces explaining the actual achievement and clearing out the misconceptions; but in short, terms like "playing god" or "creating new life from scratch" are inaccurate because technically you'd have to insert the artificial genome into a host cell and produce a viable organism, one that could replicate itself, before you'd have created life. Theoretically this isn't impossible or even particularly incredible, but it poses a whole lot of technical demands. And would this life actually really be "new" or even entirely synthetic?Aside from this, actual living organisms, "old life", are still required to carry out the essential parts of the process for us. Both E. coli bacteria and baker's yeast, Saccharomyces cerevisiae, common biological model organisms, were required in this case. They're like little biochemical factories doing the job for us, putting the artificially synthesized blocks of DNA together to form the genome, basically a bigger ring-shaped DNA molecule. It's still largely unknown how they do it. I'd also put the extra demand that this new organism would have to "do" something new in order to be called a true new organism. Its genome would have to be engineered in a way that allowed it to do something that no other living organism before it has done. Something like producing new "engineered" gene products or catalyzing new and exciting biochemical reactions. That would be seriously awesome. The J. Craig Venter institute speculates:Scientists foresee many potential positive applications including new pharmaceuticals, biologically produced (“green”) fuels, and the possibility of rapidly generating vaccines against emerging microbial diseases.So all in all it seems we are quite a bit away from "playing god". Not even when an artificial genome has been introduced into a host cell, creating a viable "new" organism, will we be even close to knowing how evolution has built genomes and how all of its parts interact to produce life. We're not making life, we're cheating by using bits and pieces of "old" life and putting it together in "new" ways. Carl Zimmer writes:When and if Venter’s team does create a viable synthetic life form, our ignorance will still remain profound. Scientists have gotten very good at manipulating genes--at copying them or using them to make biotechnology products like insulin--but they still know relatively little about how genes work together in living things.Who knows if we will ever be able to create something entirely new. But the journey there seems like a pretty decent goal all in itself. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A., Smith, H.O. (2008). Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science DOI: 10.1126/science.1151721Swedish blog tags: Vetenskap, BiologiTechnorati tags: Science, Biology, Genomics, Venter... Read more »
D Gibson, G A Benders, C Andrews-Pfannkoch, E A Denisova, H Baden-Tillson, J Zaveri, T B Stockwell, A Brownley, D W Thomas, M A Algire.... (2008) Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science. DOI: 10.1126/science.1151721
- January 27, 2010
- 05:36 PM
- 582 views
God's will and beliefs are your own, not god's
by Daniel in Ego sum Daniel
I've written before about how religious beliefs probably are grounded in brain mechanisms that we use for other purposes, primarily social interactions. There is no "god spot" in the brain, rather we think of supernatural all-powerful agents much in the same way as we think of the people we interact with. It suggests that religious belief is a secondary effect of basic or general mechanisms that guide social cognition, although it is not definitely proven. That study dealt with god's perceived involvement in the world and god's perceived emotion among other things - in a newer article published around christmas in PNAS a team of researchers have investigated how believers think when they think about god's will and god's own beliefs. The importance of such an investigation is highlighted already in the opening paragraph of the article.Religion appears to serve as a moral compass for the vast majority of people around the world. It informs whether same-sex marriage is love or sin, whether war is an act of security or of terror, and whether abortion rights represent personal liberty or permission to murder. Many religions are centered on a god (or gods) that has beliefs and intentions, with adherents encouraged to follow "God’s will" on everything from martyr-dom to career planning to voting. Within these religious systems, how do people know what their god wills?Since we already readily infer other people's beliefs egocentrically, that is as similar to our own - conservative people tend to gauge positively evaluated people as more conservative than progressive people do - it's justified to ask: How do your own beliefs guide your predictions about god's beliefs? Especially since we seem to think about god as we think about the people we interact with. According to these results believers project their own values and beliefs on their god (or gods) to a great extent, which could certainly help explain not only the great diversity and variability of religious belief and expression, but also the ambiguous nature of religious interpretation. The paper includes several studies, among them several correlational studies using surveys where people were asked to estimate god's, the "average American's", Bill Gates', George Bush's (among other known figures) beliefs on several controversial subjects such as abortion and same-sex marriage, and an experimental study where the subjects' beliefs were manipulated through exposure to persuasive arguments in order to see if they "changed god's mind" as readily as they changed their own. Most interestingly for me though, they also conducted a neuroimaging study, and since it's what I'm most familiar with I will focus on that. It consisted of 17 test subjects reporting their own attitudes on controversial subjects as exemplified above, as well as estimating the attitudes of the "average American" and god on the same subjects while in an MRI machine. Below you see three images that highlight the differences in brain region activation (yellow/orange spots) when comparing the measurements done while stating your own attitudes vs. estimation of the "average American" attitude, estimation of God's attitude vs. the "average American" attitude, and most interestingly your own attitude vs. estimation of god's attitude. Ref: N. Epley et. al. (see reference below)As you can see, there is no difference between thinking of your own beliefs and thinking about god's beliefs, which stands in contrast with how it looks when you're thinking of another person's beliefs. Of course the image only shows one representative slice of the data, but the results were consistent across the panel. Thinking about god's beliefs seems statistically indistinguishable from thinking about your own beliefs, whatever your beliefs are. The brain regions that were found to show differences in the self vs. American and god vs. American comparisons, and no differences is the self vs. god comparisons, include regions that are known to be involved in thinking about your own mental state and in the projection of your own mental states onto others. In a follow-up analysis the authors closed in on one of these regions, the medial prefrontal cortex, and observed that it had a significantly lower activity when thinking about the beliefs of the "average American" than when thinking of your own beliefs or those of god, which again were indistinguishable. Compare the three columns in figure B. BOLD is the measurement of blood oxygen level in the brain regions, which is a correlate of brain activity. There is a growing body of literature showing that religious beliefs seem to emerge from the same neural substrates that produce a more general social cognition. The interesting point in these studies is that while we relate to the entity of god and experience god's involvement in the world much like we would that of another person, our estimations of god's will and beliefs are self-referential and egocentrically biased, more so than our estimation of other people's beliefs. Religiously motivated political, moral or social stances may originate just as much from your self as from others in your surroundings, like your parents or congregation. Indeed it only seems natural to assume that god has the same belief as oneself. God, as the supreme authority, must hold true beliefs and most people naturally presume that their own beliefs are true. As an atheist one is often confronted with the view that without religion there would be no morality; that without religion humanity would degenerate. As a professed nonbeliever you're either an immoral degenerate or unconsciously religious. These data provide some evidence that morality and personal beliefs are native to human cognition and are largely independent from religious inputs. People may use religious agents as a moral compass, forming impressions and making decisions based on what they presume God as the ultimate moral authority would believe or want. The central feature of a compass, however, is that it points north no matter what direction a person is facing. This research suggests that, unlike an actual compass, inferences about God's beliefs may instead point people further in whatever direction they are already facing.PS: Just as a side note I want to mention that in one of the correlational studies they included nonbelievers. However the results were difficult to interpret. Nonbelievers seem to go less according to their own beliefs when estimating god's beliefs... which somehow makes sense but kind of doesn't prove anything. At least, the authors note, it demonstrates that you have to believe in god to make an egocentric estimation of god's beliefs in the first place.Epley N, Converse BA, Delbosc A, Monteleone GA, & Cacioppo JT (2009). Believers' estimates of God's beliefs are more egocentric than estimates of other people's beliefs. Proceedings of the National Academy of Sciences of the United States of America, 106 (51), 21533-8 PMID: 19955414Swedish blog tags: Vetenskap, Biologi, Neurovetenskap, Hjärnan, ReligionTechnorati tags: Science, Biology, Neuroscience, Brain, Religion
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Epley N, Converse BA, Delbosc A, Monteleone GA, & Cacioppo JT. (2009) Believers' estimates of God's beliefs are more egocentric than estimates of other people's beliefs. Proceedings of the National Academy of Sciences of the United States of America, 106(51), 21533-8. PMID: 19955414
- January 26, 2010
- 04:30 PM
- 575 views
E. coli do the wave
by Daniel in Ego sum Daniel
Now someone just has to engineer them to shout WOOOOOOOOAAAAH! Being able to predict recurring phenomena in the environment in order to adapt to them better offers an immense advantage to an organism. That's why pretty much all living things have an internal molecular clock that quite literally "ticks", it oscillates back and forth and allows the organism to tell what time it is. This probably arose in unicellular organisms to protect the delicate DNA molecule from the danger of UV light from the sun by timing DNA replication, when the molecule is exposed, to the nighttime hours. Having an internal clock would also allow this unicellular organism to separate different chemical reactions in time to prevent them from interacting with each other. Us multicellular organisms not only coordinate our cellular chemical reactions by time, we also adapt our behavior and our physiology. Sleep is the most dramatic example, but the release of most hormones for instance varies during the 24-hour cycle and it's also worth mentioning the many seasonal migrations that criss-cross the globe every year. In essence, time keeping is an elementary part of being alive. The authors of the paper described in the video above have managed to connect this time keeping mechanism in E. coli with a mechanism that the bacteria use to communicate with other cells in the colony, called quorum sensing, thus making the whole colony oscillate in near synchrony. This is visualized by adding the gene for green fluorescent protein into the molecular clock, something the authors reported already in 2008. The result, as you can see in the video, is a propagating wave of flashing bacteria. This is not only a beautiful demonstration of a fundamental function of all living cells, it's an elegant use of the available biotechnology and it advances the repertoire of molecular tools we have at our disposition for the creation of useful organisms in the future. Danino, T., Mondragón-Palomino, O., Tsimring, L., & Hasty, J. (2010). A synchronized quorum of genetic clocks Nature, 463 (7279), 326-330 DOI: 10.1038/nature08753Swedish blog tags: Vetenskap, Biologi, BioteknologiTechnorati tags: Science, Biology, Biotechnology, Chronobiology, E. coli
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Danino, T., Mondragón-Palomino, O., Tsimring, L., & Hasty, J. (2010) A synchronized quorum of genetic clocks. Nature, 463(7279), 326-330. DOI: 10.1038/nature08753
- May 20, 2009
- 06:11 PM
- 568 views
The ONE fossil
by Daniel in Ego sum Daniel
I don't even know where to start. The full media onslaught that is "Ida" or Darwinius masillae has been all the buzz since it was announced yesterday. Buzz, buzz. But let's start from the beginning by going directly to the source - this is from the PLoS ONE community blog:We at PLoS ONE have been kept busy over the past few weeks, as we worked hard to oversee the peer review and publication of an exciting new article by an international team of scientists, led by Dr Jørn Hurum, of the University of Oslo Natural History Museum. The other authors were: Jens Franzen, Philip Gingerich, Jörg Habersetzer, Wighart von Koenigswald and B. Holly Smith.The article, entitled, Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology, documents the discovery of a remarkably complete and well-preserved fossil of an extinct early primate in Messel Pit, Germany, a site of great significance for fossils of the Eocene epoch.The creature, named Darwinius masillae by the paper’s authors, lived an estimated 47 million years ago and is the first example of a previously unknown genus of primate. The fossil, known as “Ida,” is 95% complete and includes the skeleton, an outline of the creature’s body and the contents of her gut, allowing the researchers to reconstruct her life history and diet. Ida was an agile, young, herbivorous, female, about the size of a small monkey, who feasted on fruit and leaves in the trees of the Messel rain forest and died, aged about nine months, at the edge of a volcanic lake. Unfortunately the actual science behind the project has been overshadowed by the embarrassingly sensationalistic media strategy that accompanies it - including this website with the ridiculous tagline "The Link" and this "trailer" from the History Channel. Frankly it's a bit overwhelming to take all of it in, but there are some good or OK reports from The New York Times, BBC and The Times, and some very ghastly ones like the one from Sky News or the aforementioned trailer. For those that want a more balanced view, Carl Zimmer comments on the media hype and gathers some opinions from leading palaeontologists ("it is a rather vanilla-flavored adapiform that does not differ appreciably from other members of that well-known group of Eocene primates"); Laelaps and Pharyngula review the scientific findings, because there actually are some, and Not Exactly Rocket Science is just plain funny. It would be easy to blame the media for the hype, but it seems the scientific group that discovered and analyzed the fossil - no doubt aided by a nice team of publicists and TV producers - are behind it. It's all about the tie-ins, the book deal, the contract with National Geographic and BBC et.c. It's all business and not science. It seems like they want to force the iconic status, almost in the mold of Lucy, complete with a name and an iconic image, describing it as "an asteroid falling down to earth", "something that the world has never seen before", a "rosetta stone" of evolution, "a revolutionary scientific find that will change everything" et.c. It's ridiculous. And what's worse, the faulty reporting in the media affects the public understanding of evolution in an incredibly negative way and reinforces old misconceptions that evolutionary scientists have been working very hard to dispel. Even worse still is that it's so simple:Is Darwinius a "missing link"Don't be silly. Of course not. Nobody uses the term "missing link" in evolution. It pre-supposes evolution takes place as a linear progression between now living organisms, which is false. All organisms that ever existed and will ever exist are "missing links" between any one form and another and every gap that is filled by a "missing link" creates another 2 gaps on each side of it. All in all, the term is useless. Darwinius represents an important step in human evolutionThis perspective unjustifiably paints evolution as the process that made humans. Darwinius lived approx. 47 million years ago, the common ancestor between us humans and our closest relative, the chimpanzee, lived approx. 5-7 million years ago. Do the math. At most, Darwinius represents a transition in the evolution that eventually would lead to humans... as well as many other primates. It's not even likely that it is a direct primate ancestor. There are no surefire ways of determining if a fossil represents an organism from which a now living organism descends directly, or if it represents a "side branch". It's not even easy to do so with our closest extinct relatives like Australopithecus afarensis, much less an organism that is 47 million years old. Calling it "the earliest known human ancestor" is just preposterous. Darwinius shows the connection between humans and the rest of the animal kingdomThis really stupefies me. So, until now we had no reason to believe the human species is an animal? Darwinius might give us insight into early primate evolution, but our place within the animal tree is not disputed. This is not in debate and this is not why we look for fossils. Darwinius finally confirms the theory of evolutionThis is an atrociously unfounded statement. Everything we know abut living organisms "confirms" evolution. None of it makes sense unless there's evolution. Evolution has been confirmed times innumerable by a wealth of independent observations from many different fields. This really yanks my chain! Evolutionary theory doesn't stand and fall on transition fossils! That some of it comes from the media is expected, but that some of it comes from the scientists behind the discovery is unforgivable.Swedish blog tags: Vetenskap, Evolution, Paleontologi, Neurovetenskap, DarwiniusTechnorati tags: Science, Evolution, Paleontology, Fossil, DarwiniusFranzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723... Read more »
Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005723
- August 17, 2009
- 11:10 AM
- 540 views
The new naturalists?
by Daniel in Ego sum Daniel
Some time ago I watched a documentary called Lord of the Ants (clips available online) about the brilliant Ed O. Wilson, a born Naturalist whom I've also had the pleasure of hearing in person, and I was struck by his enthusiasm for natural history and the traditional exploratory naturalist work. It fed my imagination and made me think about my own work as a biologist. I'm probably as far away as you can come from a field biologist, working as I do with online genome databases and DNA sequences, but I realized that maybe we still have a lot in common. After watching the documentary I reached for my ever present pad of post-it notes and jolted down "a naturalist in the new world of genomes?" Note my amusement when I'm scanning through the latest issue of Bioessays and find the following passage in a commentary about recent findings in the field of transposable elements and conserved noncoding sequences (reference below). Charles Darwin and Alfred Russel Wallace were naturalists. They observed diverse landscapes, noted heritable variations within species, and suggested that challenges and opportunities in the environment would favor the fittest variants. Wallace and Darwin did not, however, understand the source of the variations in morphology that they observed. Evolutionary theory grew out of attention to this variation, but early discussions of evolution generally referred only in passing to the mechanisms that generate variation (as random mutation), and instead focused on selection and drift.It was not until the discovery of the structure of DNA, about a century after Darwin's Origin of Species was published, that the biochemistry of genetic variation could begin to be understood. However, over the course of the past decade, as genome sequences began to fill the literature, even the most molecular and computational of biologists have become like naturalists. They wander through diverse landscapes of As, Ts, Gs, and Cs, comparing genomes and wonder about the origin of the distinct classes of variation found there.That's exactly right. For everyone that has spent some time wading through what seems to be never ending stretches of genetic code from several different species, prodding and probing here and there as you go, lifting up interesting or colorful stretches of DNA sequence, looking for new exciting genes perhaps or just trying to make sense of how it all comes together and how it all relates, the likeness to an ecological system is striking. It does require a measure of curiosity and an exploratory vein. It's probably one of the most accurate descriptions of the kind of work that we do, and one that's easy to subscribe to.Caporale, L. (2009). Putting together the pieces: evolutionary mechanisms at work within genomes BioEssays, 31 (7), 700-702 DOI: 10.1002/bies.200900067
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Caporale, L. (2009) Putting together the pieces: evolutionary mechanisms at work within genomes. BioEssays, 31(7), 700-702. DOI: 10.1002/bies.200900067
- June 30, 2011
- 01:36 PM
- 539 views
The mighty coelacanth
by Daniel in Ego sum Daniel
I've added the above illustration of a Coelacanth (Latimeria chalumnae) to my collection of illustrations together with one I had already made of a lungfish (open image). If you like you can download both high-res TIF-files here. The same Creative Common license applies as described under the "Download Illustrations" tab above.
I was prompted to add the coelacanth after reading a recent fascinating article about the secretive lives of these marvelous fish (via Deep Sea News) by Dr. Hans Fricke and co-workers. The article summarizes decades of study of the Latimeria population outside the island Grande Comore in the Indian ocean.
Latimeria live in large overlapping home ranges that can be occupied for as long as 21 years. Most individuals are confined to relatively small home ranges, resting in the same caves during the day. One hundred and forty five coelacanths are individually known, and we estimate the total population size of Grande Comore as approximately 300–400 adult individuals. <...> We estimate that the mean numbers of deaths and newcomers are 3–4 individuals per year, suggesting that longevity may exceed 100 years.
I'm astounded and my imagination is fueled by the intimate detail and vivid language with which the individual lives of these fishes is described! From the re-sighting of known individuals across several decades, the description of their cave-dwellings, which their share in family groups, their nocturnal hunting habits, and how they sometimes move outside of their familiar home-ranges. You can also read this recent interview with Fricke in Wired.
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Fricke, H., Hissmann, K., Froese, R., Schauer, J., Plante, R., & Fricke, S. (2011) The population biology of the living coelacanth studied over 21 years. Marine Biology, 158(7), 1511-1522. DOI: 10.1007/s00227-011-1667-x
- June 27, 2011
- 07:24 PM
- 517 views
Nicotine, appetite and the brain
by Daniel in Ego sum Daniel
Nicotine is not only very, very addictive, as a central nervous system stimulant it can also affect our motivations and behaviors in a wider sense. One of the behaviors it can modify is appetitive behavior. It's a well-funded fact that smokers tend to have a lower body-mass than non-smokers, and that smokers who quit have a tendency to gain weight, although until now the neurobiological mechanism for this modulation was unknown.
Recent findings from two different publications reveal parts of this mechanism, but while most reports have pin-pointed the results involving appetite suppression through pro-opiomelanocortin neurons, there is evidence that the complete picture is more complicated than that.
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Mineur, Y., Abizaid, A., Rao, Y., Salas, R., DiLeone, R., Gundisch, D., Diano, S., De Biasi, M., Horvath, T., Gao, X.... (2011) Nicotine Decreases Food Intake Through Activation of POMC Neurons. Science, 332(6035), 1330-1332. DOI: 10.1126/science.1201889
Huang, H., Xu, Y., & van den Pol, A. (2011) Nicotine excites hypothalamic arcuate anorexigenic proopiomelanocortin neurons and orexigenic neuropeptide Y neurons: similarities and differences. Journal of Neurophysiology. DOI: 10.1152/jn.00740.2010
- August 28, 2009
- 09:20 AM
- 506 views
Still not "new" or "artificial"
by Daniel in Ego sum Daniel
After having headed the efforts to transplant a bacterial genome from one species to the other and to create a synthetic bacterial genome from scratch, Craig Venter predicts to finally have a synthetic species created before the end of the year. Judging by the results published in advance on the Science express website last week (find it on the print issue of Science soon), it seems his J. Craig Venter Institute (JCVI) is well on its way. In a post from last year I commented on the JCVI's creation of a synthetic Mycoplasma genitalium genome and lamented the media coverage's choice of terms ("playing god", "man-made life", "creating life from scratch", et c.) to describe the in and of themselves impressive results. I wrote:... terms like "playing god" or "creating new life from scratch" are inaccurate because technically you'd have to insert the artificial genome into a host cell and produce a viable organism, one that could replicate itself, before you'd have created life. Theoretically this isn't impossible or even particularly incredible, but it poses a whole lot of technical demands. And would this life actually really be "new" or even entirely synthetic?With these latest results it seems we're a step closer to just that, even if it still doesn't fulfill the criteria I'd use to characterize a completely new or artificial or even synthetic organism. By cloning a transformed version of a Mycoplasma mycoides genome in yeast cells, then transplanting it into a recipient cell of a closely relates species, Mycoplasma capricolum, and producing viable colonies of engineered M. mycoides, basically "re-booting" cells with a new genome (how cool is that!?), the team at JCVI developed a protocol through which it would be possible to take a completely synthetic genome, clone it and introduce it into "empty" receptor cells to produce a "new" and engineered species. The difficulty had been to successfully transplant the engineered bacterial genome from the yeast cells to the final receptor bacterial cell. The use of yeast cells to engineer the genome is essential since there are well-established genetic tools for yeast that are not available for the bacteria used. To solve this issue the team destroyed the recipient cell's defense against foreign DNA, a restriction endonuclease that cleaves foreign DNA into pieces, and modified the donor genome so that it exhibited the same methylation pattern as native M. capricolum DNA. Methylation is a secondary modification of the DNA molecule that affects gene expression and is used by bacterial cells to prevent their own DNA from being cleaved by endonucleases.It's going to be very interesting to see if JCVI will be able to combine their ability to synthesize a bacterial genome with these latest achievements to create a synthetic species before year's end. Whenever they do it, the question still remains if this would constitute "new" or "artificial" life. In my opinion it would still very much be "old life" put together in new ways, which is still a great feat and an important advance in science, don't get me wrong; but "new life" or "artificial life" are nothing by hype-y buzzwords. I've written two posts about it. The media reports this time around have so far been better than last year, without hyperbolic mentions of "playing god" or anything like that. There's the article I link to at the top of this post from The Times Online, and another at MIT's Technology Review. Meanwhile a post at a Discover Magazine blog opens with:Although scientists may not have come close to cataloging all the different kinds of life on the planet, genetics pioneer Craig Venter is pressing ahead with his plans to create biology version 2.0.Biology version 2.0!? That makes no sense whatsoever. Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N., Alperovich, N., Thomas, D., Merryman, C., Hutchison, C., Smith, H., Venter, J., & Glass, J. (2009). Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast Science DOI: 10.1126/science.1173759Swedish blog tags: Vetenskap, BiologiTechnorati tags: Science, Biology, Genomics, Venter
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Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science. DOI: 10.1126/science.1173759
- December 3, 2010
- 06:48 PM
- 506 views
My summary of NASA's arsenic-thriving bacteria story
by Daniel in Ego sum Daniel
Almost instantly after coming home from work yesterday, I noticed a steady stream of mentions of a mysterious and hugely hyped NASA press conference scheduled for later in the day trickling in via Facebook, Twitter, blogs and news sites. I got excited, but also a bit confused. NASA's announcement seemed spectacular enough:
NASA will hold a news conference at 11 a.m. PST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.
After much speculation, what we all now know was revealed at the press conference:
Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.
Source: xkcd. "According to a new paper published in the journal Science, reporters are unable to thrive in an arsenic-rich environment."
A discovery that according to NASA means that "the fundamental knowledge about what comprises all known life on Earth" has changed and that "the definition of life has just expanded". Hyperbolic much? The paper that describes these new findings was published in advance yesterday in Science, find the link at the bottom of the post, and there are indications that associated papers with more details will be published in the coming months.
It's been exciting to follow the reporting pretty much directly as it's happened and I've been Tweeting and Facebooking the story unfolding almost in real time since yesterday. All in all this story has been a great exercise in observing how online science reporting works and how blogs and social media works within this context.
By this time yesterday the furore was on:
Phil Plait's Bad Astronomy blog was very early in giving a measured but enthusiastic summary; "NASA's real news: bacterium on Earth that lives off arsenic!", so enthusiastic that a few errors, now corrected, made their way in. For the best and most sensible summary and background I would point to Carl Zimmer's excellent post "Of Arsenic and Aliens", which was posted simultaneously with NASA's press conference. Soon enough SciTech news sites started picking up the story: WIRED titled its report "NASA Finds New Arsenic-Based Life Form in California". New Scientist sank to new and lower lows with the headline "Arsenic-based bacteria point to new life forms", although they do a good job at presenting the doubts that remain about the finding. The Guardian's science pages started tracking the story pretty soon as well, posting links to the different reports as they were coming in: "Nasa unveils new life form: Bacteria that thrive on arsenic".
The somewhat fallacious tendency to call this a "new life form" becomes really apparent at this point, no doubt fueled by the sensationalistic NASA press conference and its astrobiology angle. Many reports give the impression that the arsenic-thriving bacteria represent some sort of "alternative" branch of life, or a primordially ancient form of life that we weren't aware of, which is incorrect, or that the bacteria were discovered incorporating arsenic into their cellular mechanisms in their natural environment, which is also incorrect.
Here in Sweden the major newspapers also ran spectacular headlines about the "new life form": Dagens Nyheter wrote "New life form discovered in a lake of arsenic", and Svenska Dagbladet followed with the not quite as wrong "The bacteria that lives on arsenic".
An interesting aspect in the stream of information is how the story itself has evolved since the first reports and the press conference. At first it wasn't clear from many reports if they had actually proven that the arsenic-thriving bacteria incorporated arsenic instead of phosphorus into their DNA, and what exactly the evidence was. Some reports presented doubts about the evidence, some didn't, but several have had to append or correct their information. Many still remain tentative about whether or not the evidence is sufficient to claim that arsenic was incorporated into the bacteria's DNA, not to speak of other cellular components that include phosphorus such as the cell membranes and ATP. This is all "science as usual", but the "science-report-by-press-conference" strategy doesn't exacly mirror the long and tentative process of scrutiny that all scientific findings have to go through even after publication.
I think that perhaps our demands for a clear and instant message are too high?
Aside from Carl Zimmer's post, I can recommend the following science blogger's takes on the story: Greg Laden's "NASA's new organism, the meaning of life, and Darwin's Second Theory", which focuses on the evolutionary implications, and PZ Myers' "It's not an arsenic-based life form", which very clearly describes the actual experiments and findings. Ed Yong's "Mono Lake bacteria build their DNA using arsenic (and no, this isn’t about aliens)" also adds some background to the field of study of arsenic-loving microorganisms and warns against going overboard with the conclusions.
Notice how RealScientists(TM) avoid writing about "new life forms".
In the end though, there's no doubt this is an exciting and significant finding, and the reason this will become THE scientific story of 2010, at least attention-wise, is not just because of the shrewd media strategy. Yet I can't help but being a bit cynical about the whole THIS WILL CHANGE EVERYTHING 4-EVER!!!!1 hype, especially since it very easily can lead to widespread misconceptions about biology.
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., Oremland, R.S. (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science : 10.1126/science.1197258
... Read more »
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/10.1126/science.1197258
- December 8, 2010
- 06:12 PM
- 500 views
Falsehoods associated with the arsenic-thriving bacteria story: What it is and what it isn't
by Daniel in Ego sum Daniel
>> My previous post was more of a summary of what the reporting of the "NASA arsenic-thriving bacteria" story looked like from my perspective in the wake of the massive Internet onslaught of information. In this post I want to talk about how the style of communication that drove this story has lead to the dissemination of falsehoods or misconceptions that hinder a proper understanding of biology in general, regardless of the validity of the actual findings.
The aftermath
Last week I concluded that this was an interesting story with many significant possibilities, but that doubts had been raised about the validity of the findings and the scope of the conclusions that could be drawn. Already yesterday the backlash was a fact. Carl Zimmer has called up experts in the field, as well as two of the authors of the Science paper, and summarizes the aftermath in a Slate article published earlier today: "Scientists see fatal flaws in the NASA study of arsenic-based life".
None of the scientists I spoke to ruled out the possibility that such weird bacteria might exist. <...> But almost to a person, they felt that the NASA team had failed to take some basic precautions to avoid misleading results.
Much of it centers around the review posted by Rosemary Redfield of the University of British Columbia which very clearly and methodically exposes the shortcomings of the experiments from a microbiology point of view: "Arsenic-associated bacteria (NASA's claims)". She was by no means the only one who raised serious questions soon after NASA's press conference and the publication of the scientific article in Science: Read "Arsenate-based DNA: a big idea with big holes" and "Ordinary evidence would do". The main contentions that have been raised have to do with the controls used in the experiment, the methods of detection of arsenate in DNA and other molecules, and about whether or not the researchers managed to lower the amount of phosphate enough to actually "force" the bacteria to thrive on arsenate instead.
I also concluded that this kind of aftermath is "science as usual", not something to get particularly worked up about, but that the style of communication that drove the story just doesn't allow for this process to come through. We get a mismatch between the communication of science, which affects people's expectations of science, and the actual scientific work method. This story couldn't have been better adapted for fast and enthusiastic dissemination through blogs, Twitter feeds and YouTube channels, but science isn't quite adapted to the internet... yet, and a very interesting conflict arises. A few bloggers have focused on this as well: "Extraordinary claims attract extraordinary blogging" at Byte Size Biology and "Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?" at Wired.
Falsehoods
Some of the words used to describe the findings have been grandiose to say the least. Most reports claimed that these arsenic-thriving bacteria represented some sort of "new life form". NASA claimed that "the fundamental knowledge about what comprises all known life on Earth" has changed, that "the definition of life has just expanded" and that it "will alter biology textbooks and expand the scope of the search for life beyond Earth". Even the competing journal Nature writes in a news report that this finding "is posed to overturn scientists' understanding of the biochemistry of living organisms", even though they also allow for the doubts to be voiced. Among all this hype, it's difficult to separate the actual bigger picture from the falsehoods.
The discovery of arsenic-thriving bacteria (GFAJ-1 from now on) does not expand our definition of life
Simply because biology doesn't yet have a unified working definition of what life is. I suspect it's the wrong kind of question to ask in the first place. Life is diverse even at its most central processes and the best we should try to do is to define the different "solutions" that living organisms have come up with to solve the problems posed by their environments. Within that framework the possibility of an organism that is able to incorporate arsenic into its biomolecules in phosphate-poor environments definitely represents a previously unknown, "new" and exciting solution, but to say that it expands our definition of life supposes there is a definition in the first place. Thinking in terms of solutions rather than a broad all-encompassing definition also gives a better evolutionary perspective; many solutions are shared by a great number of organisms, some are shared by smaller groups - this leads us to talk about the emergence of innovations along evolutionary history rather than about the presence or absence of life's "common denominators". This would have prevented the next falsehood I want to talk about...
GFAJ-1 doesn't represent a "new life form"
The bacterial strain GFAJ-1 could in itself be called a "new" life form, then again so could any species that's never been described before. The word "new" is more misleading than informative. In this case "new life form" is taken to mean either a species that represents a new and unknown group of bacteria, or a whole different form of life altogether; an organism completely unrelated to anything else we know, part of the so-called "shadow biosphere". The authors of the Science study have refuted these possibilities themselves: To identify the type of bacteria they had isolated, they compared the gene sequences from ribosomal subunit genes between GFAJ-1 and many other species of bacteria, and arrive at the conclusion that the arsenic-thriving strain is related to the known genus of salt-loving bacteria Halomonas. The evolutionary tree below is a visualization of the analysis and shows GFAJ-1 within the yellow-marked Halomonas group. In orange you can also see, to take the point further, that good ole E. coli is a close relative.
Ref: Adapted from Wolfe-Simon et. al. (see reference below).
The fact that this comparison of very old and very conserved genes across many bacterial species could even be done highlights the fact that GFAJ-1 does not represent a whole "other" ancestral form of life. They have ribosomes of the same origin as most other life forms on Earth.
Our fundamental knowledge of what comprises life on Earth or of the biochemistry of life hasn't changed
The perspective presented by the authors of the study is that by demonstrating that the incorporation of arsenate into biomolecules is possible in an organism, then there might be organisms that thrive on arsenate instead of phosphate somewhere on Earth, or indeed on different worlds. This somewhat hyperbolic (and it seems unfounded) supposition is what has driven NASA's astrobiology angle. However, what the authors actually claim to have demonstrated is that arsenate incorporation under extreme conditions could have evolved as a secondary solution to the problem of low phosphate availability. That is, "old life" doing something new. Or in the words of George Cody, an expert in "weird life" who also communicated with Carl Zimmer on the arsenic-thriving bacteria:
Philosophically, if it turned out that an organism could use arsenate in place of phosphate, this would not in my opinion rewrite the rules of life as we know it; aside from the hydrolysis issue, arsenate is chemically very similar to phosphate. A careful chemist could likely synthesize DNA oligomers with an arsenate backbone. As I understand it this is precisely why arsenate is a poison. Ultimately, the idea of a shadow biosphere is interesting, but it would have to be demonstrated to be truly distinct from extant b... Read more »
Wolfe-Simon, F., Switzer Blum, J., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science. info:/10.1126/science.1197258
- June 7, 2011
- 12:42 PM
- 496 views
IGFBP evolution: An interesting case of gene family expansion and retention
by Daniel in Ego sum Daniel
Or: How I really should have come up with a better title.
A small announcement: I have an article out as a first author in this month's issue of the journal Endocrinology. It's a nice journal and we spent a long time working on the manuscript so I'm very pleased that it's out. Here's a Worlde word cloud of the whole article... pretty interesting. It sums everything up pretty well actually. It's all about the evolution of the Insulin-like Growth Factor Binding Protein family of genes.
Click to see larger.
Why is it worth studying the evolutionary history of this particular gene family you might ask? It's not very well known, generally, and I bet very few know about its functions or that some members seem to be involved in certain types of cancer, for instance. Many times these gene families disappear behind esoteric acronyms and convoluted webs of functional interactions that only the initiated understand, and it's difficult to generate some sort of general interest in them. It all becomes a bit dry. But when you look a bit closer, many "obscure" (at least to the general audience) genes and proteins have a really interesting evolutionary story to tell, something that goes beyond the mere evolution of their gene sequences.
Continue after the jump »
... Read more »
Ocampo Daza D, Sundström G, Bergqvist CA, Duan C, & Larhammar D. (2011) Evolution of the Insulin-Like Growth Factor Binding Protein (IGFBP) Family. Endocrinology, 152(6), 2278-89. PMID: 21505050
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