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Dunbal>>> "There is no medical evidence that it helps prevent or cure colds, etc."

The BBC reported a year or more ago that the latest research suggests that supplements can reduce the duration of a cold once you've got it but don't do anything for prevention - my current use of Vit.C follows this, I take on orange juice and citrus fruit when I have a cold and occassionally even have tablets.

Member of the Finnish DOH and an epidemiology expert >>>"Duration of cold episodes that occurred during prophylaxis was significantly reduced in both children and adults. For children this represented an average reduction of 14% in symptom days, while in adults the reduction was 8%."

See http://medicine.plosjournals.org/perlserv/?request =get-document&doi=10.1371/journal.pmed.0020168; also http://www.quackwatch.org/01QuackeryRelatedTopics/ DSH/colds.html is a slightly less positive review that still agrees that duration can be reduced by supplementing ascorbic acid intake.

That all sounds like it "helps ... cure colds" to me.

If asexual clades displayed the same pattern of discrete variation as sexual clades, this would challenge traditional view that sex is necessary for diversification into species.

Here is the original article in PLoS Biology. Why link to a story in the Times when the original is available in an open access online journal?

As this study shows, biologists avoid using the word "evolution" in their research proposals and reports presumably because they do not want to alienate the current US government, which is a major source of grants. So scientists clearly can be influenced, at least in which words they use to report it if not in the underlying research, by the perceived biases of government bodies which fund them.

The prediction then would be that during the Bush administration we should have seen a marked decrease in mentions of "global warming" and "climate change" in grant applications and published research. But our self-proclaimed "suppressed scholar" is claiming something quite contradictory: Both that scientists say what their funders want (with the US government being the largest single funder of basic scientific research), and also that current scientists have a biased towards claims for "global warming" and "climate change," rather than favoring the bias of the current US government against these topics - which is at least as strong its bias against "evolution."

WTF? The only logical conclusion from the (somewhat justified) claim that scientists show favor towards their funders' biases is that global climate change is more of a threat than the current scientific consensus (at least among American scientists) portrays.

Appropriately, on the front-page of that web site, http://biology.plosjournals.org/ , there is an article entitled "Splicing and protein evolution".

The study of biology was already open source. There is a wealth of data at the NCBI and other sources. We are seeing a renaissance in molecular biology right now and I, for one, attribute it to the hard work of thousands of researchers freely sharing their work. It's not just the data either, it's journals and software, too. We have more information than we know how to handle, and it's being created much faster than it will ever be understood. It's gotten to a point where new fields of study are being created just to interpret the collected data and try to make some sense of it. Bioinformatics and computational biology are truly amazing fields, the only trouble is attempting to explain just what it is you do to friends and relatives. Trust me, it's not always easy.

What - are you going for the incomprehensible babble award? Is the joke wooshing over my head?

evolution of man and squirrel alike indeed continued apace until ~approx 100 000 years ago, when modern man first left Africa and the laws of evolution ceased to apply to humans, due to the plasticity of spandrels.

The "laws of evolution" are still with us, and spandrels are not necessarily plastic. Nor does the presence of spandrels lead to plasticity at all. I think you're just joining evolutionary-sciency words to sound clever.

Hence, positing evolution of humanity is incorrect in timespans extending much further back than a mere 6000 years.

Skin color? This must have arisen in the last 150kya after humans moved out of Africa. I could list other examples, but it's quite obvious you're talking out your arse here.

It is hard to determine if this study and many other recent similar ones implying recent evolution in humans are driven by mere ignorance or if more sinister motives are at work.

Yes. It appears that this study was funded by the evil Dairy-conglomerate to promote milk-drinking behavior.

The author referenced here, one Nicholas Wade, is notable for engaging in ideologically dubious activities

Nicholas Wade is a very well respected science writer. I guess that science could be consided "ideologically dubious" to some.

Convergent adaptation of human lactase persistence in Africa and Europe


A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits--animal domestication and adult milk consumption.

You can get it fron Nature Genetics if you have institutional access.

If you want to know why Lactose tolerance is a big deal read this (mainly because it's a nice example of Gene-Culture co-evolution).

--Simon

It appears that they are drawing a target around an arrow instead of using real science, just telling a story of some hippie Neanderthals. Although I do see similarities. No Evidence of Neanderthal mtDNA Contribution to Early Modern Humans http://biology.plosjournals.org/perlserv?request=g et-document&doi=10.1371/journal.pbio.0020057 Although Germany has been very proud of their dead Neanderthal monkeys, and England has been envious of German for them.. They are not human.

Take a look at this article of recent evolution in homo sapiens over the last 10,000 years.
A layperson's summary.
The actual publication.

You need professional help, mutilator. I mean what is it with you people and circumcision? Its like the crazed muslims and their hatred for women or something. Go back to the middle ages where you belong please. Irritation aside, you made a good and well informed post besides that, which I found interesting. But I'd thank you to get off the slicing little boys penises bandwagon.

If all of that work and expense could be done by one company, and any other company could snap it up w/o having to invest in that research, then who in their right mind would invest 10's or 100's of millions of dollars into producing a product when that basically means they're giving it to their competetors for free? Sometimes when the product is sufficiently narrow in scope, even with patents, on a successful drug, drug companies fail to recover their investment during the patent's lifetime.

An essay regarding the mentioned topic, and I thought it might be interesting to a few people. The are many non-technical paragraphs that draw to the author's conclusions, and those should be readable by all.

http://medicine.plosjournals.org/perlserv?request= get-document&doi=10.1371/journal.pmed.0020124

Summary:

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field.

In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.

I believe there was some problem explaining to natives in Africa what it means to be in a double-blind test involving placebos. I don't believe these PREP trials are highly regarded by everyone, see here: http://medicine.plosjournals.org/perlserv/?request =get-document&doi=10.1371/journal.pmed.0020234 Just and FYI...

PC fantasy, sorry. Nobody working in cognetive science, neurology, or, for that matter, designing 'unbiased' tests for employment would agree with you.

As an example, I give you the paper in question. People learnt long ago not to spell it out too clearly, but look up MCPH1 or CDK5RAP2 and you'll find that they are related to brain function.

The PLOS biology article is available to everyone via Open Access.

Life on Earth 'unlikely to have emerged in volcanic springs'

13 Feb 2006

"The latest findings of experiments to re-create the conditions under which life could emerge from chemical reactions suggest that volcanic springs and marine hydrothermal events are unlikely to have provided the right environment, a leading researcher from the United States will tell an international meeting tomorrow (14 February 2006) at the Royal Society, the UK national academy of science."

In the alternative Plos ran an interestin article titled Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks which touches on the front running theories on the origin of life.

Similar mechanisms are at work during the process of insight, as shown in a recent PLOS biology paper (summary here). According to this research, insight is primarily a right-hemispheric process involving very "holistic" thinking about a problem. Interestingly, it is accompanied by suppression of incoming activity from the environment, as though giving the brain free reign to free-associate, we are able to more efficiently search the entire solution space.

Of course not. The reason geeks have all the hot women is that this "analytical-autistic" deformation happens to be a kind of "extreme male brain". It is an exaggeration of the most tangible differences between (most) female brains and (most) male brains.

Have a look at this essay at PLoS Biology, which is mostly based on Baron-Cohen's results, and which seems to be causing quite a stir at the moment.

So next time your conversation dries up, rejoice, for this is a shining proof of your extreme virility ! :D

Thomas-

Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks gives a quick overview and update on the most recent research.

The paper was published in an Open Access journal so you can all browse that if the press release is too basic. Go to http://genetics.plosjournals.org/perlserv/?request =get-document&doi=10.1371/journal.pgen.0010065

As the title of the article says, they show that isolated human neutrophils are capable of killing Anthrax. The mechanism is unusuual, the spores are first eaten by the neutrophils. Then the spores germinate inside the cells to a form of bacteria that are readily killed (vegitative) as opposed to the virulent, disease causing form which is formed in the outside environment.

However, they don't look directly at animal models - so the leap of faith is that the lung infection is bad when the spores do not elicit a neutrophil response. How the spores avoid eliciting a host response in lung is the bigger question, which is not addressed by the paper.

[Evolution] provides a plausible explanation for the origin of species, but has no predictive power at all.

How come even a cursory glance at the recent articles in the open access PLoS journals reveal lots of people making predictions from evolutionary information?

Protein Molecular Function Prediction by Bayesian Phylogenomics

Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses

Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions

Fools! Don't they know that evolution has no predictive power at all?

[Evolution] provides a plausible explanation for the origin of species, but has no predictive power at all.

How come even a cursory glance at the recent articles in the open access PLoS journals reveal lots of people making predictions from evolutionary information?

Protein Molecular Function Prediction by Bayesian Phylogenomics

Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses

Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions

Fools! Don't they know that evolution has no predictive power at all?

[Evolution] provides a plausible explanation for the origin of species, but has no predictive power at all.

How come even a cursory glance at the recent articles in the open access PLoS journals reveal lots of people making predictions from evolutionary information?

Protein Molecular Function Prediction by Bayesian Phylogenomics

Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses

Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions

Fools! Don't they know that evolution has no predictive power at all?

The advent of better genetic maps has allowed scientists to more accurately time the emergence of the delta32 CCR5 mutation. It now appears that this allele emerged earlier than previously thought and has not been strongly selected by plague. In other words, its frequency in Northern Europeans is explained by 'random', neutral selection and is not markedly different from other genes in the genome. (See here for more details)

Small molecule inhibitors that block the interaction between HIV and susceptible host cells show promise. Two huge concerns -- 1) HIV is not absolutely dependent on CCR5 usage. During chronic infection (presumably, when many CCR5+ cells have already been depleted), HIV can utilize an alternate coreceptor, CXCR4, to mediate entry into a cell. CXCR4-using viruses tend to be more aggressive than CCR5 viruses, and it is possible that CCR5 inhibitors would drive the more rapid emergence of these CXCR4-using strains. 2) Even though CCR5 inhibitors target a conserved, functionally essential target, HIV can still become resistant to these inhibitors.

is how this mutation got into the general population in the first place.

The current operating theory, as I understand it, is that it originated (uhhh ... mutated?) somewhere in southern Finland, made it's way across the Baltic Sea to Sweden, and from there fanned out across Europe and West Asia during the period of Viking expansion -- from about the 8th-10th centuries.

The mutation is found in native populations as far away as Cyprus and North Africa; but the closer you get to Scandinavia, the more prevalent it becomes. So, really, the Vikings were doing the rest of Europe a public service while they were casually burning it into the ground.

Plunder. The gift that keeps on giving

Note that these findings are published in the freely available, creative commons licensed journal PLoS Biology:

Entire issues are offered as beautiful PDFs. From the PLoS site http://www.plosjournals.org/:

PLoS publishes peer-reviewed, open-access scientific and medical journals that include original research as well as timely feature articles. All PLoS articles are immediately freely accessible online, deposited in the free public archive PubMed Central, and can be redistributed and reused according to the terms of the Creative Commons Attribution License.

Note that these findings are published in the freely available, creative commons licensed journal PLoS Biology:

Entire issues are offered as beautiful PDFs. From the PLoS site http://www.plosjournals.org/:

PLoS publishes peer-reviewed, open-access scientific and medical journals that include original research as well as timely feature articles. All PLoS articles are immediately freely accessible online, deposited in the free public archive PubMed Central, and can be redistributed and reused according to the terms of the Creative Commons Attribution License.

http://medicine.plosjournals.org/perlserv/?request =slideshow&type=table&doi=10.1371/journal.pmed.002 0124&id=4104this table seems to be the most interesting part of it all, showing what effort should be done to get a PPV (positive predictive value) above 50%. This is specifically aimed at clinical studies, BTW, people with anti-evolutionist feelings have nothing to see here ;)

Furthermore, as an essay, it might or might not be peer reviewed, didn't go into that. The study itself is probably not as crappy as you might think after reading the New Scientist link, because, as parent makes clear, it provides a modeling approach to assess articles in this field.

I read the study, available here: http://biology.plosjournals.org/perlserv/?request= get-document&doi=10.1371/journal.pbio.0030299

The class of compounds being researched does have the potential for being better than amphetamines and other stimulants because of its selectivity for brain function affected by sleep deprivation.

This could, potentially, mean fewer side effects and less addiction than other stimulants.

There is also further research to be done regarding the use of this class of compounds to treat non-sleep-deprivation related decreased neuro function. Brain damage due to Alzheimer's comes to mind, and might have been mentioned in the article.

Finally, look for compounds in this class to be used to make people "better than well" for selected reasons -- airline pilots, truck drivers, baseball players, etc. It will still be several years, perhaps decades, before compounds in this class make it to your pharmacy.

And I don't believe the United States ever had wild horses: I think they were all brought here.

Belief is nice, but often facts smack it upside the ass. North America had mammoths, mastodons, sabre-toothed tigers, camels, and -- yes -- horses. In fact, horses evolved in North America and only later spread to Eurasia. The locals went extict 11,000 years ago.

As far as we know, native North American horses were never domesticated. The domesticable wild mustangs were just feral horses brought over by the conquistadors.

PDF files are very useful to distribute printable materials, such as books, spec sheets, PR and corporate bullshit (ugh), brochures, etc

HTML can be used in the same roles, and without loss of functionality

So far -- and it's been some years now since PDF arrived -- I've never seen a single PDF document that I thought needed to be a PDF document.

From a webpage on Molecular Insights into Human Brain Evolution by Jane Bradbury, the following quote applies:

"For natural selection to work, the costs of brain evolution must be outweighed by the advantages gained in terms of fitness. For many years, explains ecological psychologist Robin Dunbar (University of Liverpool, United Kingdom), "people thought that the ability to hunt or forage better was what drove the evolution of our brains. But a better diet had to come before we could grow a bigger brain." Dunbar believes instead that brain evolution in primates and more generally in mammals "has been driven by the need to manage social relationships, and in primates, in particular, to coordinate coherence in social groups through time and space". More complex social interactions, he says, mean that individuals are better able to pool resources to solve problems like finding food, and so they survive better."

Finally, our most unique and advanced feature -- consciousness -- is explained. Carter describes the "working memory" model developed by Alan Baddeley, where images and speech-based information is held for short time in a cache-like space, while the "central executive" part co-ordinates the information processing.

Coincidentally, today the journal PLoS Biology released an article, where researchers describe a neuronal model they've devised of certain aspects of consciousness.

Synopsis (for the layman): Assessing Consciousness: Of Vigilance and Distractedness

Research paper: Ongoing Spontaneous Activity Controls Access to Consciousness: A Neuronal Model for Inattentional Blindness

In general, Stanislas Dehaene (one of the paper's authors) has some very cool publications on neuroscience, consciousness, cognition, and so forth. You can find them here.

Here's a quote from the aforementioned synopsis:

Have you ever walked smack into a parking meter or tripped over something on the sidewalk? Embarrassing as such incidents may be, they're the product of normal brain function. The brain is continuously bombarded with sensory information about the environment but perceives just a fraction of these inputs. The rest--pertinent details or not--is filtered out. It's thought that consciousness emerges from the activity of multiple spontaneous neural processors that run in parallel and connect to a higher order cognitive network that mediates the conscious perception. But this higher order network has limited processing capacity. That means if you're distracted, your brain can't accommodate additional sensory information, like "there's a parking meter in front of you, look out!"

To understand how spontaneous brain processing interacts with higher order cognition, Stanislas Dehaene and Jean-Pierre Changeux modeled the dynamic properties of brain activity with computer simulations. Their simulations show that while spontaneous brain activity sometimes facilitates processing, more often it competes with external stimuli for access to consciousness. Intriguingly, the results of the computer simulations very closely match physiological and psychophysical experimental data and thus shed new light on how intrinsic brain activity modulates conscious perception. ...

With higher vigilance states, weaker external stimuli are able to ignite the global workspace. But paying attention to one thing narrows your perceptive capacity. Once ignited by one stimulus, the network cannot consciously process any others. Dehaene and Changeux propose that spontaneous activity--which operates within an "anatomically distinct set of workplace neurons"--offers an organism a measure of autonomy relative to the external world. While this decoupling of internal thought and external stimuli does have its disadvantages--like that pesky parking meter--it also provides the opportunity for introspection and creativity, which the authors argue is likely to "play a crucial role in the spontaneous generation of novel, flexible behavior."

Finally, our most unique and advanced feature -- consciousness -- is explained. Carter describes the "working memory" model developed by Alan Baddeley, where images and speech-based information is held for short time in a cache-like space, while the "central executive" part co-ordinates the information processing.

Coincidentally, today the journal PLoS Biology released an article, where researchers describe a neuronal model they've devised of certain aspects of consciousness.

Synopsis (for the layman): Assessing Consciousness: Of Vigilance and Distractedness

Research paper: Ongoing Spontaneous Activity Controls Access to Consciousness: A Neuronal Model for Inattentional Blindness

In general, Stanislas Dehaene (one of the paper's authors) has some very cool publications on neuroscience, consciousness, cognition, and so forth. You can find them here.

Here's a quote from the aforementioned synopsis:

Have you ever walked smack into a parking meter or tripped over something on the sidewalk? Embarrassing as such incidents may be, they're the product of normal brain function. The brain is continuously bombarded with sensory information about the environment but perceives just a fraction of these inputs. The rest--pertinent details or not--is filtered out. It's thought that consciousness emerges from the activity of multiple spontaneous neural processors that run in parallel and connect to a higher order cognitive network that mediates the conscious perception. But this higher order network has limited processing capacity. That means if you're distracted, your brain can't accommodate additional sensory information, like "there's a parking meter in front of you, look out!"

To understand how spontaneous brain processing interacts with higher order cognition, Stanislas Dehaene and Jean-Pierre Changeux modeled the dynamic properties of brain activity with computer simulations. Their simulations show that while spontaneous brain activity sometimes facilitates processing, more often it competes with external stimuli for access to consciousness. Intriguingly, the results of the computer simulations very closely match physiological and psychophysical experimental data and thus shed new light on how intrinsic brain activity modulates conscious perception. ...

With higher vigilance states, weaker external stimuli are able to ignite the global workspace. But paying attention to one thing narrows your perceptive capacity. Once ignited by one stimulus, the network cannot consciously process any others. Dehaene and Changeux propose that spontaneous activity--which operates within an "anatomically distinct set of workplace neurons"--offers an organism a measure of autonomy relative to the external world. While this decoupling of internal thought and external stimuli does have its disadvantages--like that pesky parking meter--it also provides the opportunity for introspection and creativity, which the authors argue is likely to "play a crucial role in the spontaneous generation of novel, flexible behavior."

PLoS Biology had a very neat article on using fMRI in courtrooms last year, fMRI Beyond the Clinic: Will It Ever Be Ready for Prime Time?. The first couple of paragraphs:

Functional magnetic resonance imaging--fMRI--opens a window onto the brain at work. By tracking changes in cerebral blood flow as a subject performs a mental task, fMRI shows which brain regions "light up" when making a movement, thinking of a loved one, or telling a lie. Its ability to reveal function, not merely structure, distinguishes fMRI from static neuroimaging techniques such as CT scanning, and its capacity to highlight the neural substrates of decisions, emotions, and deceptions has propelled fMRI into the popular consciousness. Discussions of the future of fMRI have conjured visions of mind-reading devices used everywhere from the front door at the airport terminal to the back room of the corporate personnel office. At least one "neuromarketing" research firm is already trying to use fMRI to probe what consumers "really" think about their clients' products.

But will fMRI's utility in the real world ever match the power we currently imagine for it? Is fMRI likely to leave the clinic for widespread use in the courtroom or the boardroom? Are there neuroethical nightmares just around the corner? Or are all these vivid specters really just idle speculations that will never come to pass?