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Weiye Loh

Cancer resembles life 1 billion years ago, say astrobiologists - microbiology, genomics... - 0 views

www.lifescientist.com.au/..._years_ago_say_astrobiologists

Cancer Evolution Life

shared by Weiye Loh on 17 Feb 11 - No Cached
  • astrobiologists, working with oncologists in the US, have suggested that cancer resembles ancient forms of life that flourished between 600 million and 1 billion years ago.
  • Read more about what this discovery means for cancer research.
  • The genes that controlled the behaviour of these early multicellular organisms still reside within our own cells, managed by more recent genes that keep them in check.It's when these newer controlling genes fail that the older mechanisms take over, and the cell reverts to its earlier behaviours and grows out of control.
  • ...11 more annotations...
  • The new theory, published in the journal Physical Biology, has been put forward by two leading figures in the world of cosmology and astrobiology: Paul Davies, director of the Beyond Center for Fundamental Concepts in Science, Arizona State University; and Charles Lineweaver, from the Australian National University.
  • According to Lineweaver, this suggests that cancer is an atavism, or an evolutionary throwback.
  • In the paper, they suggest that a close look at cancer shows similarities with early forms of multicellular life.
  • “Unlike bacteria and viruses, cancer has not developed the capacity to evolve into new forms. In fact, cancer is better understood as the reversion of cells to the way they behaved a little over one billion years ago, when humans were nothing more than loose-knit colonies of only partially differentiated cells. “We think that the tumours that develop in cancer patients today take the same form as these simple cellular structures did more than a billion years ago,” he said.
  • One piece of evidence to support this theory is that cancers appear in virtually all metazoans, with the notable exception of the bizarre naked mole rat."This quasi-ubiquity suggests that the mechanisms of cancer are deep-rooted in evolutionary history, a conjecture that receives support from both paleontology and genetics," they write.
  • the genes that controlled this early multi-cellular form of life are like a computer operating system's 'safe mode', and when there are failures or mutations in the more recent genes that manage the way cells specialise and interact to form the complex life of today, then the earlier level of programming takes over.
  • Their notion is in contrast to a prevailing theory that cancer cells are 'rogue' cells that evolve rapidly within the body, overcoming the normal slew of cellular defences.
  • However, Davies and Lineweaver point out that cancer cells are highly cooperative with each other, if competing with the host's cells. This suggests a pre-existing complexity that is reminiscent of early multicellular life.
  • cancers' manifold survival mechanisms are predictable, and unlikely to emerge spontaneously through evolution within each individual in such a consistent way.
  • The good news is that this means combating cancer is not necessarily as complex as if the cancers were rogue cells evolving new and novel defence mechanisms within the body.Instead, because cancers fall back on the same evolved mechanisms that were used by early life, we can expect them to remain predictable, thus if they're susceptible to treatment, it's unlikely they'll evolve new ways to get around it.
  • If the atavism hypothesis is correct, there are new reasons for optimism," they write.
  • Weiye Loh on 17 Feb 11
     
    Feature: Inside DNA vaccines bioMD makes a bid for Andrew Forest's Allied Medical and Coridon Alexion acquires technology for MoCD therapy More > Most Popular Media Releases Cancer resembles life 1 billion years ago, say astrobiologists Feature: The challenge of a herpes simplex vaccine Feature: Proteomics power of pawpaw bioMD makes a bid for Andrew Forest's Allied Medical and Coridon Immune system boosting hormone might lead to HIV cure Biotechnology Directory Company Profile Check out this company's profile and more in the Biotechnology Directory! Biotechnology Directory Find company by name Find company by category Latest Jobs Senior Software Developer / Java Analyst Programm App Support Developer - Java / J2ee Solutions Consultant - VIC Technical Writer Product Manager (Fisheye/Crucible)   BUYING GUIDES Portable Multimedia Players Digital Cameras Digital Video Cameras LATEST PRODUCTS HTC Wildfire S Android phone (preview) Panasonic LUMIX DMC-GH2 digital camera HTC Desire S Android phone (preview) Qld ICT minister Robert Schwarten retires Movie piracy costs Aus economy $1.37 billion in 12 months: AFACT Wireless smartphones essential to e-health: CSIRO Aussie outsourcing CRM budgets to soar in 2011: Ovum Federal government to evaluate education revolution targets Business continuity planning - more than just disaster recovery Proving the value of IT - Part one 5 open source security projects to watch In-memory computing Information security in 2011 EFA shoots down 'unproductive' AFACT movie piracy study In Pictures: IBM hosts Galactic dinner Emerson Network Power launches new infrastructure solutions Consumers not smart enough for smartphones? Google one-ups Apple online media subscription service M2M offerings expand as more machines go online India cancels satellite spectrum deal after controversy Lenovo profit rises in Q3 on strong PC sales in China Taiwan firm to supply touch sensors to Samsung HP regains top position in India's PC market Copyright 20
Weiye Loh

Sunita Narain: Indian scientists: missing in action - 0 views

www.business-standard.com/...428350

Science Policy Capitalism

shared by Weiye Loh on 15 Mar 11 - No Cached
  • Since then there has been dead silence among the powerful scientific leaders of the country, with one exception. Kiran Karnik, a former employee of ISRO and board member of Deva
  • when the scientists who understand the issue are not prepared to engage with the public, there can be little informed discussion. The cynical public, which sees scams tumble out each day, believes easily that everybody is a crook. But, as I said, the country’s top scientists have withdrawn further into their comfort holes, their opinion frozen in contempt that Indian society is scientifically illiterate. I can assure you in the future there will be even less conversation between scientists and all of us in the public sphere.
  • This is not good. Science is about everyday policy. It needs to be understood and for this it needs to be discussed and deliberated openly and strenuously. But how will this happen if one side — the one with information, knowledge and power — will not engage in public discourse?
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  • I suspect Indian scientists have retired hurt to the pavilion. They were exposed to some nasty public scrutiny on a deal made by a premier science research establishment, Indian Space Research Organisation (ISRO), with Devas, a private company, on the allocation of spectrum. The public verdict was that the arrangement was a scandal; public resources had been given away for a song. The government, already scam-bruised, hastily scrapped the contract.
  • Take the issue of genetically-modified (GM) crops. For long this matter has been decided inside closed-door committee rooms, where scientists are comforted by the fact that their decisions will not be challenged. Their defence is “sound science” and “superior knowledge”. It is interesting that the same scientists will accept data produced by private companies pushing the product. Issues of conflict of interest will be brushed aside as integrity cannot be questioned behind closed doors. Silence is the best insurance. This is what happened inside a stuffy committee room, where scientists sat to give permission to Mahyco-Monsanto to grow genetically-modified brinjal.
  • This case involved a vegetable we all eat. This was a matter of science we had the right to know about and to decide upon. The issue made headlines. The reaction of the scientific fraternity was predictable and obnoxious. They resented the questions. They did not want a public debate.
  • As the controversy raged and more people got involved, the scientists ran for cover. They wanted none of this messy street fight. They were meant to advise prime ministers and the likes, not to answer simple questions of people. Finally, when environment minister Jairam Ramesh took the decision on the side of the ordinary vegetable eater, unconvinced by the validity of the scientific data to justify no-harm, scientists were missing in their public reactions. Instead, they whispered about lack of “sound science” in the decision inside committees.
  • The matter did not end there. The minister commissioned an inter-academy inquiry — six top scientific institutions looked into GM crops and Bt-brinjal — expecting a rigorous examination of the technical issues and data gaps. The report released by this committee was shoddy to say the least. It contained no references or attributions and not a single citation. It made sweeping statements and lifted passages from a government newsletter and even from global biotech industry. The report was thrashed. Scientists again withdrew into offended silence.
  • The final report of this apex-science group is marginally better in that it includes citations but it reeks of scientific arrogance cloaked in jargon. The committee did not find it fit to review the matter, which had reached public scrutiny. The report is only a cover for their established opinion about the ‘truth’ of Bt-brinjal. Science for them is certainly not a matter of enquiry, critique or even dissent.
  • the world has changed. No longer is this report meant only for top political and policy leaders, who would be overwhelmed by the weight of the matter, the language and the expert knowledge of the writer. The report will be subjected to public scrutiny. Its lack of rigour will be deliberated, its unquestioned assertion challenged.
  • This is the difference between the manufactured comfortable world of science behind closed doors and the noisy messy world outside. It is clear to me that Indian scientists need confidence to creatively engage in public concerns. The task to build scientific literacy will not happen without their engagement and their tolerance for dissent. The role of science in Indian democracy is being revisited with a new intensity. The only problem is that the key players are missing in action.
Weiye Loh

It's Even Less in Your Genes by Richard C. Lewontin | The New York Review of Books - 0 views

www.nybooks.com/...its-even-less-your-genes

Genetic Nature Nurture Diversity

shared by Weiye Loh on 17 May 11 - No Cached
  • One of the complications is that the effective environment is defined by the life activities of the organism itself.
  • Thus, as organisms evolve, their environments necessarily evolve with them. Although classic Darwinism is framed by referring to organisms adapting to environments, the actual process of evolution involves the creation of new “ecological niches” as new life forms come into existence. Part of the ecological niche of an earthworm is the tunnel excavated by the worm and part of the ecological niche of a tree is the assemblage of fungi associated with the tree’s root system that provide it with nutrients.
  • , the distinction between organisms and their environments remains deeply embedded in our consciousness. Partly this is due to the inertia of educational institutions and materials
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  • But the problem is deeper than simply intellectual inertia. It goes back, ultimately, to the unconsidered differentiations we make—at every moment when we distinguish among objects—between those in the foreground of our consciousness and the background places in which the objects happen to be situated. Moreover, this distinction creates a hierarchy of objects. We are conscious not only of the skin that encloses and defines the object, but of bits and pieces of that object, each of which must have its own “skin.” That is the problem of anatomization. A car has a motor and brakes and a transmission and an outer body that, at appropriate moments, become separate objects of our consciousness, objects that at least some knowledgeable person recognizes as coherent entities.
  • Evelyn Fox Keller sees “The Mirage of a Space Between Nature and Nurture” as a consequence of our false division of the world into living objects without sufficient consideration of the external milieu in which they are embedded, since organisms help create effective environments through their own life activities.
  • The central point of her analysis has been that gender itself (as opposed to sex) is socially constructed, and that construction has influenced the development of science:If there is a single point on which all feminist scholarship…has converged, it is the importance of recognizing the social construction of gender…. All of my work on gender and science proceeds from this basic recognition. My endeavor has been to call attention to the ways in which the social construction of a binary opposition between “masculine” and “feminine” has influenced the social construction of science.
  • major critical concern of Fox Keller’s present book is the widespread attempt to partition in some quantitative way the contribution made to human variation by differences in biological inheritance, that is, differences in genes, as opposed to differences in life experience. She wants to make clear a distinction between analyzing the relative strength of the causes of variation among individuals and groups, an analysis that is coherent in principle, and simply assigning the relative contributions of biological and environmental causes to the value of some character in an individual
  • It is, for example, all very well to say that genetic variation is responsible for 76 percent of the observed variation in adult height among American women while the remaining 24 percent is a consequence of differences in nutrition. The implication is that if all variation in nutrition were abolished then 24 percent of the observed height variation among individuals in the population in the next generation would disappear. To say, however, that 76 percent of Evelyn Fox Keller’s height was caused by her genes and 24 percent by her nutrition does not make sense. The nonsensical implication of trying to partition the causes of her individual height would be that if she never ate anything she would still be three quarters as tall as she is.
  • In fact, Keller is too optimistic about the assignment of causes of variation even when considering variation in a population. As she herself notes parenthetically, the assignment of relative proportions of population variation to different causes in a population depends on there being no specific interaction between the causes.
  • Keller’s rather casual treatment of the interaction between causal factors in the case of the drummers, despite her very great sophistication in analyzing the meaning of variation, is a symptom of a fault that is deeply embedded in the analytic training and thinking of both natural and social scientists. If there are several variable factors influencing some phenomenon, how are we to assign the relative importance to each in determining total variation? Let us take an extreme example. Suppose that we plant seeds of each of two different varieties of corn in two different locations with the following results measured in bushels of corn produced (see Table 1). There are differences between the varieties in their yield from location to location and there are differences between locations from variety to variety. So, both variety and location matter. But there is no average variation between locations when averaged over varieties or between varieties when averaged over locations. Just by knowing the variation in yield associated with location and variety separately does not tell us which factor is the more important source of variation; nor do the facts of location and variety exhaust the description of that variation.
  • Weiye Loh on 17 May 11
     
    In trying to analyze the natural world, scientists are seldom aware of the degree to which their ideas are influenced both by their way of perceiving the everyday world and by the constraints that our cognitive development puts on our formulations. At every moment of perception of the world around us, we isolate objects as discrete entities with clear boundaries while we relegate the rest to a background in which the objects exist.
lee weiting

designer babies - 0 views

groups.diigo.com/...new-media-ethics-2009-course

genetic engineering designer baby

shared by lee weiting on 21 Oct 09 - No Cached
  • lee weiting on 21 Oct 09
     
    this topic will be discussed in the presentation in class. However, i feel that maybe i should also start a discussion here regarding the topic on designer baby. This is an article regarding designer baby. Designer baby has raised many ethical issues, such as the right of fetus etc. Many people are against designer baby. However this article points out an advantage of designer baby that is to save sick people. if it can save a live, i do not think is unethical to do it. On the other hand, i will think is unethical if one knows of the presence of some serious genetic mutation and still choose to pass it on to the future generation. i think the most basic form of ethics is not to do harm to people whenever possible. strive for a balance, strive for the best. In my point of view, this is what determine if an action is ethical or not. from this perspective, i will think that designer baby is ethical and should be allowed. Any other views? =)
lo sokwan

Scientists decode human genome's instruction manual - 0 views

www.guardian.co.uk/...entists-epigenome-manual-genes

shared by lo sokwan on 20 Oct 09 - Cached
  • lo sokwan on 20 Oct 09
     
    I'm pretty disturbed that there is now a genetic formula to "make" healthy humans. Though it sounds pretty cool that future human beings can be 'perfectly healthy', but at the same time, it is pretty weird to imagine a world without illnesses. Could this lead to a commodification of human beings? If it is only available to the wealthy or the elite groups,is it an ethical technology?
  • Jody Poh on 20 Oct 09
     
    This is interesting. I think that the technology itself is neutral. Yes, it does open up options that pushes our boundary of what we consider ethical. But eventually, it is how humans use the technology that makes it ethical or unethical. Personally, I think that if this works out, it will definitely be only available to the wealthy and elite as they are the ones that have more means to access the technology. Just something to think about, expensive medication is also more accessible and available to the wealthy and elite. Then is it ethical then to manufacture expensive medication? haha just some thoughts:)
  • Weiye Loh on 21 Oct 09
     
    I think the issue with genetic research is that it legalizes the (scientific) claim of eugenics, perhaps when taken to the extreme allows for some kind of Nazi style ethnic cleansing. Arthur Kroker wrote a pretty interesting, albeit rather doomsday prophetic account on this topic. I do not agree fully with him but I like the way he writes (rather enigmatic and seductive), about how science and the human genome project has managed to immunize itself from the overt fascism of second-wave eugenics of National Socialism. The book is available in the library "The will to technology and the culture of nihilism". It'll be nice to know what you all think about it. Do you think that such science will one day turn against humans who are deemed to be lesser human simply because they have 'bad' genes?
Weiye Loh

Skepticblog » The Linus Pauling effect - 0 views

skepticblog.org/...the-linus-pauling-effect

HIV_AIDS Denial Science Falsifiability

shared by Weiye Loh on 14 Apr 11 - No Cached
  • So if syphilis causes AIDS, and not HIV, where is the evidence? As microbiologist and epidemiolist Tara Smith points out in her excellent blog, Margulis offers none. Instead, she says to the credulous and uncritical interviewer: The idea that penicillin kills the cause of the disease is nuts. If you treat the painless chancre in the first few days of infection, you may stop the bacterium before the symbiosis develops, but if you really get syphilis, all you can do is live with the spirochete. The spirochete lives permanently as a symbiont in the patient. The infection cannot be killed because it becomes part of the patient’s genome and protein synthesis biochemistry. After syphilis establishes this symbiotic relationship with a person, it becomes dependent on human cells and is undetectable by any testing. Great. Just what we need: an untestable hypothesis promoted by assertion and reputation, not something concrete that scientists could test (although most specialists in microbiology would say the evidence is clear that the HIV retrovirus, and not the spirochaete bacterium Treponema pallidum, is the true cause of AIDS).
  • Has she never actually LOOKED at the hundreds of peer-reviewed scientific papers documenting the structure of the HIV virus, and the clear documentation of that virus in patients that suffer and die from AIDS? Or the fact that patients treated with anti-retrovirals manage to suppress their AIDS symptoms? Or the disaster in South Africa, when the government became active AIDS deniers, spread misinformation and myths about AIDS, and the infection rate shot up? Not even the hard-core AIDS deniers like Peter Duesberg deny that the HIV virus exists!
  • she slips outside the realm of science entirely, and becomes a full-fledged AIDS denier. My jaw just dropped when I read the following: There is a vast body of literature on syphilis spanning from the 1500s until after World War II, when the disease was supposedly cured by penicillin. It’s in our paper “Resurgence of the Great Imitator.” Our claim is that there’s no evidence that HIV is an infectious virus, or even an entity at all. There’s no scientific paper that proves that the HIV virus causes AIDS. Kary Mullis said in an interview that he went looking for a reference substantiating that HIV causes AIDS and discovered, “There is no such document.”
  • Weiye Loh on 14 Apr 11
     
    The phenomenon is a familiar one: let's call it "the Linus Pauling effect." A highly respected and honored senior scientist, largely out of the mainstream and not up to date with the recent developments (and perhaps a bit senile), makes weird pronouncements about their pet ideas-and the press, so used to giving celebrities free air time for any junk they wish to say, prints and publishes it all as if it is the final truth. The great Linus Pauling may have won two Nobel Prizes, but his crazy idea that megadoses of Vitamin C would cure nearly everything seems to have died with him. William Shockley may have won a Nobel for his work on transistors, but his racist ideas about genetics (a field in which he had no expertise) should never been taken seriously. Kary Mullis may have deserved his Nobel Prize for developing the polymerase chain reaction, but that gives him no qualifications to speak with authority on his unscientific ideas about AIDS denial and global warming and astrology (he hits the trifecta for pseudoscientific woo).
Weiye Loh

Open Letter to Richard Dawkins: Why Are You Still In Denial About Group Selection? : Ev... - 0 views

scienceblogs.com/..._letter_to_richard_dawkins.php

Evolution Science

shared by Weiye Loh on 30 Sep 10 - No Cached
  • Dear Richard, I do not agree with the cynical adage "science progresses--funeral by funeral", but I fear that it might be true in your case for the subject of group selection.
  • Edward Wilson was misunderstanding kin selection as far back as Sociobiology, where he treated it as a subset of group selection ... Kin selection is not a subset of group selection, it is a logical consequence of gene selection. And gene selection is (everything that Nowak et al ought to mean by) 'standard natural selection' theory: has been ever since the neo-Darwinian synthesis of the 1930s.
  • I do not agree with the Nowak et al. article in every respect and will articulate some of my disagreements in subsequent posts. For the moment, I want to stress how alone you are in your statement about group selection. Your view is essentially pre-1975, a date that is notable not only for the publication of Sociobiology but also a paper by W.D. Hamilton, one of your heroes, who correctly saw the relationship between kin selection and group selection thanks to the work of George Price. Ever since, knowledgeable theoretical biologists have known that inclusive fitness theory includes the logic of multilevel selection, which means that altruism is selectively disadvantageous within kin groups and evolves only by virtue of groups with more altruists contributing more to the gene pool than groups with fewer altruists. The significance of relatedness is that it clusters the genes coding for altruistic and selfish behaviors into different groups.
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  • Even the contemporary theoretical biologists most critical of multilevel selection, such as Stuart West and Andy Gardner, acknowledge what you still deny. In an earlier feature on group selection published in Nature, Andy Gardner is quoted as saying "Everyone agrees that group selection occurs"--everyone except you, that is.
  • You correctly say that gene selection is standard natural selection theory. Essentially, it is a popularization of the concept of average effects in population genetics theory, which averages the fitness of alternative genes across all contexts to calculate what evolves in the total population. For that reason, it is an elementary mistake to regard gene selection as an alternative to group selection. Whenever a gene evolves in the total population on the strength of group selection, despite being selectively disadvantageous within groups, it has the highest average effect compared to the genes that it replaced. Please consult the installment of my "Truth and Reconciliation for Group Selection" series titled "Naïve Gene Selectionism" for a refresher course. While you're at it, check out the installment titled "Dawkins Protests--Too Much".
  • The Nowak et al. article includes several critiques of inclusive fitness theory that need to be distinguished from each other. One issue is whether inclusive fitness theory is truly equivalent to explicit models of evolution in multi-group populations, or whether it makes so many simplifying assumptions that it restricts itself to a small region of the parameter space. A second issue is whether benefiting collateral kin is required for the evolution of eusociality and other forms of prosociality. A third issue is whether inclusive fitness theory, as understood by the average evolutionary biologist and the general public, bears any resemblance to inclusive fitness theory as understood by the cognoscenti.
  • Weiye Loh on 30 Sep 10
     
    Open Letter to Richard Dawkins: Why Are You Still In Denial About Group Selection?
Weiye Loh

Arsenic bacteria - a post-mortem, a review, and some navel-gazing | Not Exactly Rocket ... - 0 views

blogs.discovermagazine.com/...a-review-and-some-navel-gazing

Journalism Ethics Science Biology

shared by Weiye Loh on 11 Dec 10 - No Cached
  • t was the big news that wasn’t. Hyperbolic claims about the possible discovery of alien life, or a second branch of life on Earth, turned out to be nothing more than bacteria that can thrive on arsenic, using it in place of phosphorus in their DNA and other molecules. But after the initial layers of hype were peeled away, even this extraordinar
  • This is a chronological roundup of the criticism against the science in the paper itself, ending with some personal reflections on my own handling of the story (skip to Friday, December 10th for that bit).
  • Thursday, December 2nd: Felisa Wolfe-Simon published a paper in Science, claiming to have found bacteria in California’s Mono Lake that can grow using arsenic instead of phosphorus. Given that phosphorus is meant to be one of six irreplaceable elements, this would have been a big deal, not least because the bacteria apparently used arsenic to build the backbones of their DNA molecules.
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  • In my post, I mentioned some caveats. Wolfe-Simon isolated the arsenic-loving strain, known as GFAJ-1, by growing Mono Lake bacteria in ever-increasing concentrations of arsenic while diluting out the phosphorus. It is possible that the bacteria’s arsenic molecules were an adaptation to the harsh environments within the experiment, rather than Mono Lake itself. More importantly, there were still detectable levels of phosphorus left in the cells at the end of the experiment, although Wolfe-Simon claimed that the bacteria shouldn’t have been able to grow on such small amounts.
  • signs emerged that NASA weren’t going to engage with the criticisms. Dwayne Brown, their senior public affairs officer, highlighted the fact that the paper was published in one of the “most prestigious scientific journals” and deemed it inappropriate to debate the science using the same media and bloggers who they relied on for press coverage of the science. Wolfe-Simon herself tweeted that “discussion about scientific details MUST be within a scientific venue so that we can come back to the public with a unified understanding.”
  • Jonathan Eisen says that “they carried out science by press release and press conference” and “are now hypocritical if they say that the only response should be in the scientific literature.” David Dobbs calls the attitude “a return to pre-Enlightenment thinking”, and rightly noted that “Rosie Redfield is a peer, and her blog is peer review”.
  • Chris Rowan agreed, saying that what happens after publication is what he considers to be “real peer review”. Rowan said, “The pre-publication stuff is just a quality filter, a check that the paper is not obviously wrong – and an imperfect filter at that. The real test is what happens in the months and years after publication.”Grant Jacobs and others post similar thoughts, while Nature and the Columbia Journalism Review both cover the fracas.
  • Jack Gilbert at the University of Chicago said that impatient though he is, peer-reviewed journals are the proper forum for criticism. Others were not so kind. At the Guardian, Martin Robbins says that “at almost every stage of this story the actors involved were collapsing under the weight of their own slavish obedience to a fundamentally broken… well… ’system’” And Ivan Oransky noted that NASA failed to follow its own code of conduct when announcing the study.
  • Dr Isis said, “If question remains about the voracity of these authors findings, then the only thing that is going to answer that doubt is data.  Data cannot be generated by blog discussion… Talking about digging a ditch never got it dug.”
  • it is astonishing how quickly these events unfolded and the sheer number of bloggers and media outlets that became involved in the criticism. This is indeed a brave new world, and one in which we are all the infamous Third Reviewer.
  • I tried to quell the hype around the study as best I could. I had the paper and I think that what I wrote was a fair representation of it. But, of course, that’s not necessarily enough. I’ve argued before that journalists should not be merely messengers – we should make the best possible efforts to cut through what’s being said in an attempt to uncover what’s actually true. Arguably, that didn’t happen although to clarify, I am not saying that the paper is rubbish or untrue. Despite the criticisms, I want to see the authors respond in a thorough way or to see another lab attempt replicate the experiments before jumping to conclusions.
  • the sheer amount of negative comment indicates that I could have been more critical of the paper in my piece. Others have been supportive in suggesting that this was more egg on the face of the peer reviewers and indeed, several practicing scientists took the findings on face value, speculating about everything from the implications for chemotherapy to whether the bacteria have special viruses. The counter-argument, which I have no good retort to, is that peer review is no guarantee of quality, and that writers should be able to see through the fog of whatever topic they write about.
  • my response was that we should expect people to make reasonable efforts to uncover truth and be skeptical, while appreciating that people can and will make mistakes.
  • it comes down to this: did I do enough? I was certainly cautious. I said that “there is room for doubt” and I brought up the fact that the arsenic-loving bacteria still contain measurable levels of phosphorus. But I didn’t run the paper past other sources for comment, which I typically do it for stories that contain extraordinary claims. There was certainly plenty of time to do so here and while there were various reasons that I didn’t, the bottom line is that I could have done more. That doesn’t always help, of course, but it was an important missed step. A lesson for next time.
  • I do believe that it you’re going to try to hold your profession to a higher standard, you have to be honest and open when you’ve made mistakes yourself. I also think that if you cover a story that turns out to be a bit dodgy, you have a certain responsibility in covering the follow-up
  • A basic problem with is the embargo. Specifically that journalists get early access, while peers – other specialists in the field – do not. It means that the journalist, like yourself, can rely only on the original authors, with no way of getting other views on the findings. And it means that peers can’t write about the paper when the journalists (who, inevitably, do a positive-only coverage due to the lack of other viewpoints) do, but will be able to voice only after they’ve been able to digest the paper and formulate a response.
  • No, that’s not true. The embargo doens’t preclude journalists from sending papers out to other authors for review and comment. I do this a lot and I have been critical about new papers as a result, but that’s the step that I missed for this story.
Weiye Loh

It's Only A Theory: From the 2010 APA in Boston: Neuropsychology and ethics - 0 views

itisonlyatheory.blogspot.com/...in-boston-neuropsychology.html

Ethics Neuropsychology

shared by Weiye Loh on 04 Jan 11 - No Cached
  • Joshua Greene from Harvard, known for his research on "neuroethics," the neurological underpinnings of ethical decision making in humans. The title of Greene's talk was "Beyond point-and-shoot morality: why cognitive neuroscience matters for ethics."
  • What Greene is interested in is to find out to what factors moral judgment is sensitive to, and whether it is sensitive to the relevant factors. He presented his dual process theory of morality. In this respect, he proposed an analogy with a camera. Cameras have automatic (point and shoot) settings as well as manual controls. The first mode is good enough for most purposes, the second allows the user to fine tune the settings more carefully. The two modes allow for a nice combination of efficiency and flexibility.
  • The idea is that the human brain also has two modes, a set of efficient automatic responses and a manual mode that makes us more flexible in response to non standard situations. The non moral example is our response to potential threats. Here the amygdala is very fast and efficient at focusing on potential threats (e.g., the outline of eyes in the dark), even when there actually is no threat (it's a controlled experiment in a lab, no lurking predator around).
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  • Delayed gratification illustrates the interaction between the two modes. The brain is attracted by immediate rewards, no matter what kind. However, when larger rewards are eventually going to become available, other parts of the brain come into play to override (sometimes) the immediate urge.
  • Greene's research shows that our automatic setting is "Kantian," meaning that our intuitive responses are deontological, rule driven. The manual setting, on the other hand, tends to be more utilitarian / consequentialist. Accordingly, the first mode involves emotional areas of the brain, the second one involves more cognitive areas.
  • The evidence comes from the (in)famous trolley dilemma and it's many variations.
  • when people refuse to intervene in the footbridge (as opposed to the lever) version of the dilemma, they do so because of a strong emotional response, which contradicts the otherwise utilitarian calculus they make when considering the lever version.
  • psychopaths turn out to be more utilitarian than normal subjects - presumably not because consequentialism is inherently pathological, but because their emotional responses are stunted. Mood also affects the results, with people exposed to comedy (to enhance mood), for instance, more likely to say that it is okay to push the guy off the footbridge.
  • In a more recent experiment, subjects were asked to say which action carried the better consequences, which made them feel worse, and which was overall morally acceptable. The idea was to separate the cognitive, emotional and integrative aspects of moral decision making. Predictably, activity in the amygdala correlated with deontological judgment, activity in more cognitive areas was associated with utilitarianism, and different brain regions became involved in integrating the two.
  • Another recent experiment used visual vs. verbal descriptions of moral dilemmas. Turns out that more visual people tend to behave emotionally / deontologically, while more verbal people are more utilitarian.
  • studies show that interfering with moral judgment by engaging subjects with a cognitive task slows down (though it does not reverse) utilitarian judgment, but has no effect on deontological judgment. Again, in agreement with the conclusion that the first type of modality is the result of cognition, the latter of emotion.
  • Nice to know, by the way, that when experimenters controlled for "real world expectations" that people have about trolleys, or when they used more realistic scenarios than trolleys and bridges, the results don't vary. In other words, trolley thought experiments are actually informative, contrary to popular criticisms.
  • What factors affect people's decision making in moral judgment? The main one is proximity, with people feeling much stronger obligations if they are present to the event posing the dilemma, or even relatively near (a disaster happens in a nearby country), as opposed to when they are far (a country on the other side of the world).
  • Greene's general conclusion is that neuroscience matters to ethics because it reveals the hidden mechanisms of human moral decision making. However, he says this is interesting to philosophers because it may lead to question ethical theories that are implicitly or explicitly based on such judgments. But neither philosophical deontology nor consequentialism are in fact based on common moral judgments, seems to me. They are the result of explicit analysis. (Though Greene raises the possibility that some philosophers engage in rationalizing, rather than reason, as in Kant's famously convoluted idea that masturbation is wrong because one is using oneself as a mean to an end...)
  • this is not to say that understanding moral decision making in humans isn't interesting or in fact even helpful in real life cases. An example of the latter is the common moral condemnation of incest, which is an emotional reaction that probably evolved to avoid genetically diseased offspring. It follows that science can tell us that three is nothing morally wrong in cases of incest when precautions have been taken to avoid pregnancy (and assuming psychological reactions are also accounted for). Greene puts this in terms of science helping us to transform difficult ought questions into easier ought questions.
Weiye Loh

The Biology of Politics: What Makes a Liberal or a Conservative? - TIME Healthland - 0 views

healthland.time.com/...akes-a-liberal-or-conservative

Biology Politics

shared by Weiye Loh on 21 Dec 10 - No Cached
  • There are aspects of our lives that we like to think are totally under our control — political affiliation is certainly one of them. But a growing field of researchers asserts that there may be some biology underpinning our liberal or conservative bent.
  • this sort of theory doesn't sit well with some onlookers. Hibbing describes himself as "kicked around" because of his research: "People are usually pretty proud of their political beliefs," he says. "They think they're rational responses to the world around them, so to come along and say maybe there are these predispositions that you're not even aware of ... that doesn't really go down all that well."
  • "On the left, people don't like to think that maybe people aren't fully malleable," he says. "On the right, it's that these are a bunch of liberal academics trying to show that conservatives are genetically or physiologically flawed."
  • ...1 more annotation...
  • Both sides are anxious to see how the field of the biology of politics will be viewed in 50 years — if it has indeed been lumped in with pseudosciences like phrenology or if it has become a new platform for widespread, interdisciplinary study. Meanwhile, the fascination — and vitriol — will likely remain. "The notion of where political ideology comes from has never been contested," says Bruce Bimber, a professor at University of California, Santa Barbara, who tackles this topic in graduate seminars. "It's always been a settled assumption that it is the product of socialization and life experience, and this research has come along saying, 'Wait a minute, wait a minute. We might have had this partly wrong all along.'"
Weiye Loh

The curious double standards of Simon Singh - Telegraph Blogs - 0 views

blogs.telegraph.co.uk/...ouble-standards-of-simon-singh

Skepticism Journalism Science Global Warming AGW Chiropractic

shared by Weiye Loh on 29 Jan 11 - No Cached
  • Simon Singh as in the popular mathematician and bestselling author of Fermat’s Last Theorem. And also, more germanely to this story, the recent victim of an expensive libel action brought against him by the British Chiropractic Association (BCA). The BCA eventually dropped its action – but not before Singh had run up £200,000 in legal costs. Though some it his lawyers will be able to claim back, he’s still likely to lose £60,000 of his own money as a result of his brave, principled decision to fight the case rather than cave in earlier. I hugely respected him for what he did. He won a victory (albeit a financially Pyrrhic one) not just for himself but for all those of us who trade in robust opinion and who believe that English libel laws are outrageously biased in favour of vexatious complainants, which is why we have unfortunately become a haven for libel tourists, some of them representing unspeakable causes.
  • Among those “serious matters of public interest”, you might imagine, would be Climate Change.
  • Yet in the opinion of Singh, the worldwide Climate Change industry is the one area where the robust scepticism and empiricism he professes to believe in just doesn’t apply. Apparently, the job of a journalist is just to accept the word of “the scientists” and take it as read that being as they are “scientists” their word is God and it brooks no questioning or dissent. That’s it. Finished.
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  • I have no doubt whatsoever that Sir Paul Nurse knows more about genetics than I do. It is, after all, where the field in which he won his Nobel prize. As for science, sure, Nurse has the advantage over me there, too. He has a PhD. He’s a science graduate and I’m an arts graduate. But then I’ve never pretended otherwise. My case is not that I “James Delingpole have taken a long hard look at the science of global warming and discovered through careful sifting of countless peer-reviewed papers that the experts have got it all wrong.”
  • What I am saying, and I say almost every day, is that the evidence is not as robust as the “consensus” scientists claim; that there are many distinguished scientists all round the world who dispute this alleged “consensus”; that true science doesn’t advance through “consensus” and never has; that the Climategate emails threw the peer-review process into serious doubt by demonstrating how eminently corruptable it is; that there are many vested interests out there determined and able to spend a great deal of money by making out that the case for catastrophic, man-made global warming is much stronger than it is. And on these specific issues I can reasonably claim to be better informed than Sir Paul Nurse, regardless of how many PhDs he has, because I’ve spent much more time than he has researching them and because they are not issues which require an exclusively scientific knowledge to understand. They just require the basic journalistic skill of being able to read and analyse.
Weiye Loh

Editorial Policies - 0 views

www.arjournals.com/...index.php

Science Academic Journal Academic Research

shared by Weiye Loh on 21 Feb 11 - Cached
  • More than 60% of the experiments fail to produce results or expected discoveries. From an objective point of view, this high percentage of “failed “ research generates high level pieces of knowledge. Generally, all these experiments have not been published anywhere as they have been considered useless for our research target. The objective of “The All Results Journals: Biology” focuses on recovering and publishing these valuable pieces of information in Biology. These key experiments must be considered vital for the development of science. They  are the catalyst for a real science-based empirical knowledge.
  • The All Results Journals: Biology is an online journal that publishes research articles after a controlled peer review. All articles will be published, without any barriers to access, immediately upon acceptance.
  • Every single contribution submitted to The All Results Journals and selected for a peer-review will be sent to, at least, one reviewer, though usually could be sent to two or more independent reviewers, selected by the editors and sometimes by more if further advice is required (e.g., on statistics or on a particular technique). Authors are welcome to suggest suitable independent reviewers and may also request the journal to exclude certain individuals or laboratories.
  • ...1 more annotation...
  • The journal will cover negative (or “secondary”) experiments coming from all disciplines of Biology (Botany, Cell Biology, Genetics, Ecology, Microbiology, etc). An article in The All Results Journals should be created to show the failed experiments tuning methods or reactions. Articles should present experimental discoveries, interpret their significance and establish perspective with respect to earlier work of the author. It is also advisable to cite the work where the experiments has already been tuned and published.
  • Weiye Loh on 21 Feb 11
     
    More than 60% of the experiments fail to produce results or expected discoveries. From an objective point of view, this high percentage of "failed " research generates high level pieces of knowledge. Generally, all these experiment
Weiye Loh

Roger Pielke Jr.'s Blog: Intolerance: Virtue or Anti-Science "Doublespeak"? - 0 views

rogerpielkejr.blogspot.com/...ce-virtue-or-anti-science.html

Science Skepticism Tolerance Alternative Pseudo-Science

shared by Weiye Loh on 19 Feb 11 - No Cached
  • John Beddington, the Chief Scientific Advisor to the UK government, has identified a need to be "grossly intolerant" of certain views that get in the way of dealing with important policy problems: We are grossly intolerant, and properly so, of racism. We are grossly intolerant, and properly so, of people who [are] anti-homosexuality... We are not—and I genuinely think we should think about how we do this—grossly intolerant of pseudo-science, the building up of what purports to be science by the cherry-picking of the facts and the failure to use scientific evidence and the failure to use scientific method. One way is to be completely intolerant of this nonsense. That we don't kind of shrug it off. We don't say: ‘oh, it's the media’ or ‘oh they would say that wouldn’t they?’ I think we really need, as a scientific community—and this is a very important scientific community—to think about how we do it.
  • Fortunately, Andrew Stirling, research director of the Science Policy Research Unit (which these days I think just goes by SPRU) at the University of Sussex, provides a much healthier perspective: What is this 'pseudoscience'? For Beddington, this seems to include any kind of criticism from non-scientists of new technologies like genetically modified organisms, much advocacy of the 'precautionary principle' in environmental protection, or suggestions that science itself might also legitimately be subjected to moral considerations. Who does Beddington hold to blame for this "politically or morally or religiously motivated nonsense"? For anyone who really values the central principles of science itself, the answer is quite shocking. He is targeting effectively anyone expressing "scepticism" over what he holds to be 'scientific' pronouncements—whether on GM, climate change or any other issue. Note, it is not irrational "denial" on which Beddington is calling for 'gross intolerance', but the eminently reasonable quality of "scepticism"! The alarming contradiction here is that organised, reasoned, scepticism—accepting rational argument from any quarter without favour for social status, cultural affiliations  or institutional prestige—is arguably the most precious and fundamental quality that science itself has (imperfectly) to offer. Without this enlightening aspiration, history shows how society is otherwise all-too-easily shackled by the doctrinal intolerance, intellectual blinkers and authoritarian suppression of criticism so familiar in religious, political, cultural and media institutions.
  • tirling concludes: [T]he basic aspirational principles of science offer the best means to challenge the ubiquitously human distorting pressures of self-serving privilege, hubris, prejudice and power. Among these principles are exactly the scepticism and tolerance against which Beddington is railing (ironically) so emotionally! Of course, scientific practices like peer review, open publication and acknowledgement of uncertainty all help reinforce the positive impacts of these underlying qualities. But, in the real world, any rational observer has to note that these practices are themselves imperfect. Although rarely achieved, it is inspirational ideals of universal, communitarian scepticism—guided by progressive principles of reasoned argument, integrity, pluralism, openness and, of course, empirical experiment—that best embody the great civilising potential of science itself. As the motto of none other than the Royal Society loosely enjoins (also sometimes somewhat ironically) "take nothing on authority". In this colourful instance of straight talking then, John Beddington is himself coming uncomfortably close to a particularly unsettling form of unscientific—even (in a deep sense) anti-scientific—'double speak'.
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  • Anyone who really values the progressive civilising potential of science should argue (in a qualified way as here) against Beddington's intemperate call for "complete intolerance" of scepticism. It is the social and human realities shared by politicians, non-government organisations, journalists and scientists themselves, that make tolerance of scepticism so important. The priorities pursued in scientific research and the directions taken by technology are all as fundamentally political as other areas of policy. No matter how uncomfortable and messy the resulting debates may sometimes become, we should never be cowed by any special interest—including that of scientific institutions—away from debating these issues in open, rational, democratic ways. To allow this to happen would be to undermine science itself in the most profound sense. It is the upholding of an often imperfect pursuit of scepticism and tolerance that offer the best way to respect and promote science. Such a position is, indeed, much more in keeping with the otherwise-exemplary work of John Beddington himself.Stirling's eloquent response provides a nice tonic to Beddington's unsettling remarks. Nonetheless, Beddington's perspective should be taken as a clear warning as to the pathological state of highly politicized science these days.
Weiye Loh

Genomic analysis shows humans evolved with few sweeping changes - 0 views

arstechnica.com/...-with-few-sweeping-changes.ars

Evolution Genetic

shared by Weiye Loh on 25 Feb 11 - No Cached
  • Humans and chimpanzees split around five million years ago. Ever since then, we (and they) have changed a bit to adapt to the different environments we invaded and created, and the "classic selective sweep" model was widely thought to account for these changes at the molecular level. In this scenario, a new, strongly beneficial mutation increases in frequency so rapidly that it "sweeps" away all other variants at that gene and nearby sites. Yet it is difficult to detect the evidence of such sweeps in genomic data. After analyzing 179 human genomes, an international team of researchers have concluded that these sweeps were much rarer than previously thought, and were therefore probably not a huge influence on human adaptation over the past 250,000 years. Their work is reported in Science.
Weiye Loh

YouTube - X-Men: Science Can Build Them, But Is It Ethical? - 0 views

www.youtube.com/watch

Bioethics Genetics

shared by Weiye Loh on 01 Jun 11 - No Cached
  • Weiye Loh on 01 Jun 11
     
    Is science capable of enhancing human abilities to the extent of the powers of the X-Men? What are the ethical implications if this is possible? Asa Griggs Candler Professor of Bioethics Paul Root Wolpe explores these questions raised by X-Men: First Class.
Weiye Loh

CultureLab: Thoughts within thoughts make us human - 0 views

www.newscientist.com/...in-thoughts-make-us-human.html

Language Thinking Technology

shared by Weiye Loh on 05 Jun 11 - No Cached
  • Corballis reckons instead that the thought processes that made language possible were non-linguistic, but had recursive properties to which language adapted: "Where Chomsky views thought through the lens of language, I prefer to view language though the lens of thought." From this, says Corballis, follows a better understanding of how humans actually think - and a very different perspective on language and its evolution.
  • So how did recursion help ancient humans pull themselves up by their cognitive bootstraps? It allowed us to engage in mental time travel, says Corballis, the recursive operation whereby we recall past episodes into present consciousness and imagine future ones, and sometimes even insert fictions into reality.
  • theory of mind is uniquely highly developed in humans: I may know not only what you are thinking, says Corballis, but also that you know what I am thinking. Most - but not all - language depends on this capability.
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  • Corballis's theories also help make sense of apparent anomalies such as linguist and anthropologist Daniel's Everett's work on the Pirahã, an Amazonian people who hit the headlines because of debates over whether their language has any words for colours, and, crucially, numbers. Corballis now thinks that the Pirahã language may not be that unusual, and cites the example of other languages from oral cultures, such as the Iatmul language of New Guinea, which is also said to lack recursion.
  • The emerging point is that recursion developed in the mind and need not be expressed in a language. But, as Corballis is at pains to point out, although recursion was critical to the evolution of the human mind, it is not one of those "modules" much beloved of evolutionary psychologists, many of which are said to have evolved in the Pleistocene. Nor did it depend on some genetic mutation or the emergence of some new neuron or brain structure. Instead, he suggests it came of progressive increases in short-term memory and capacity for hierarchical organisation - all dependent in turn on incremental increases in brain size.
  • But as Corballis admits, this brain size increase was especially rapid in the Pleistocene. These incremental changes can lead to sudden more substantial jumps - think water boiling or balloons popping. In mathematics these shifts are called catastrophes. So, notes Corballis, wryly, "we may perhaps conclude that the emergence of the human mind was catastrophic". Let's hope that's not too prescient.
  • Weiye Loh on 05 Jun 11
     
    His new book, The Recursive Mind: The origins of human language, thought, and civilization, is a fascinating and well-grounded exposition of the nature and power of recursion. In its ultra-reasonable way, this is quite a revolutionary book because it attacks key notions about language and thought. Most notably, it disputes the idea, argued especially by linguist Noam Chomsky, that thought is fundamentally linguistic - in other words, you need language before you can have thoughts.
Weiye Loh

Biomimicry: How Scientists Emulate Nature to Create Sustainable Designs | The Utopianis... - 0 views

utopianist.com/...-to-create-sustainable-designs

Biology Biomimetics Biomimicry Human

shared by Weiye Loh on 18 Jun 11 - No Cached
  • “The core idea is that nature, imaginative by necessity, has already solved many of the problems we are grappling with. Animals, plants, and microbes are the consummate engineers. They have found what works, what is appropriate, and most important, what lasts here on Earth. This is the real news of biomimicry: After 3.8 billion years of research and development, failures are fossils, and what surrounds us is the secret to survival. Like the viceroy butterfly imitating the monarch, we humans are imitating the best adapted organisms in our habitat. We are learning, for instance, how to harness energy like a leaf, grow food like a prairie, build ceramics like an abalone, self-medicate like a chimp, create color like a peacock, compute like a cell, and run a business like a hickory forest.”
  • A more recent example of biomimetics in action is a biological laser created by two physicists at Harvard Medical School. Malte Gather and Seok Hyun Yun placed a single cell, genetically engineered to produce green fluorescent proteins originally found in jellyfish, into a cavity with two parallel mirrors on either side. When they exposed the cell to pulses of light, it emitted green fluorescent light that focused into a laser beam with the aid of the parallel mirrors. As Gather and Yun pointed out in their paper, the single-cell biological laser avoids the use of “artificial or engineered optical gain materials, such as doped crystals, semiconductors, synthetic dyes and purified gases.”
  • Weiye Loh on 18 Jun 11
     
    if one of our goals as a species is longevity, we may want to humble ourselves and take a look at how other species manage to live symbiotically with the earth instead of just on it. Biomimetics, or biomimicry, does just that.
Weiye Loh

The Failure of Liberal Bioethics - NYTimes.com - 1 views

douthat.blogs.nytimes.com/...e-failure-of-liberal-bioethics

Bioethics

shared by Weiye Loh on 20 Aug 11 - No Cached
  • There are three broad camps in contemporary debates over bioethics. In the name of human rights and human dignity, “bio-conservatives” tend to support restricting, regulating and stigmatizing the technologies that allow us to create, manipulate and destroy embryonic life. In the name of scientific progress and human freedom, “bio-libertarians” tend to oppose any restrictions on what individuals, doctors and researchers are allowed to do. Then somewhere in between are the anguished liberals, who are uncomfortable with what they see as the absolutism of both sides, and who tend to argue that society needs to decide where to draw its bioethical lines not based on some general ideal (like “life” or “choice”), but rather case by case by case — accepting this kind of abortion but not that kind; this use of embryos but not that use; existing developments in genetic engineering but not, perhaps, the developments that await us in the future.
  • at least in the United States, the liberal effort to (as the Goodman of 1980 put it) “monitor” and “debate” and “control” the development of reproductive technologies has been extraordinarily ineffectual. From embryo experimentation to selective reduction to the eugenic uses of abortion, liberals always promise to draw lines and then never actually manage to draw them. Like Dr. Evans, they find reasons to embrace each new technological leap while promising to resist the next one — and then time passes, science marches on, and they find reasons why the next moral compromise, too, must be accepted for the greater good, or at least tolerated in the name of privacy and choice. You can always count on them to worry, often perceptively, about hypothetical evils, potential slips down the bioethical slope. But they’re either ineffectual or accommodating once an evil actually arrives. Tomorrow, they always say — tomorrow, we’ll draw the line. But tomorrow never comes.
  • Weiye Loh on 20 Aug 11
     
    The Failure of Liberal Bioethics; http://t.co/6QrUPkl
guanyou chen

How to Build A Dinosaur - 3 views

Dinosaurs ethics genetic engineering chicken

started by guanyou chen on 22 Oct 09 no follow-up yet
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