Imaging Geek

A Death, and Rebirth

2010-10-15T09:20:00.002-04:00

This will likely be my last post in this blog. A lack of time on my part, plus a commitment to another on-line project, has left me bereft of the time I need to make this thing work.

I do have a new-ish blog, over at Molecular Station. If you like what you see here, you may like what I have over there.

Farewell

Brya

Anti-vaxer gets smacked down - hard!

2010-06-25T12:09:00.004-04:00

As my one or two readers know, I am greatly opposed to the anti-vaxers and their lies. I've always found their promotion of unproven, often dangerous treatments to be particularity vexing - basically, they sell substances of little or no value (often harmful) to desperate parents. They are the snake-oil salesmen of our day.

Finally, the FDA seems to be cracking down on these thugs. Boyd Haley - second only in infamy to the king quack Andrew Wakefield has for the past few years sold an industrial chemical called N1,N3-bis(2-mercaptoethyl)isophthalamide (Boyd calls it ORS1 to make it less scary to his ~~patients~~ victims). OSR1 is an industrial chemical whose purpose is to remove certain metal ions from chemical preparations.

Boyd sells it as a mercury chealator - yes, Boyd is one of these "the mercury in vaccines cause autism" dudes, despite the fact that mercury has been removed from all childhood vax. He sells it despite the fact it has established toxicities beyond that acceptable for drugs, and despite the fact it has not ever been tested in a clinical trial for efficacy or safety. He tried to get around the law by claiming it was a "nutritional supplement".

The FDA shut him down this week. Orac, over at Respectful Insolence, has a detailed breakdown of why. But the long and short is:

OSR1 does not meet the definition of a dietary supplement, therefore it is illegal to sell it as such
Boyd makes specific biochemical claims (i.e. helps maintain a healthy glutathione level), and since the compound is intended to modify the bodies actions, is classified as a drug
This compound has not been tested as drugs need to be (clinical trials and all that), therefore it is illegal to sell it to people
Boyd claims OSR1 can treat a variety of conditions which cannot be self-diagnosed. Therefore even if OSR1 was a valid drug it would be illegal to sell it over-the-counter
Boyd conducted some animals tests, which showed OSR1 to be toxic to the immune system, pancreas, and to show general signs of whole-body toxicity. He falsely represents this in his adds, saying "OSR#1 is without detectable toxicity". It's illegal to lie about side effects.

Long story short - Boyd is illegally selling an untested drug for treating children, is illegally advertising it as a nutritional supplement, is illegally hiding known toxicities, and is illegally selling a compound by mail-order which if it functions as advertised would be a prescription drug.

With luck, he will go to jail for his illegal activities.

One down, 50,000 to go...

Genes ahoy!

2010-06-10T10:43:00.008-04:00

It's been a while since my last blog post - in my defense She Who Must Be Obeyed is preggers, so my times been consumed prepping for the arrival of my son/daughter (by which I mean I've been freaking out - its scary, being responsible for someone other than yourself).

Despite that, a bit of science came out today that is worth spreading - we now have a detailed genetic map of autism - as in we've now identified most of the mutations which lead to autistic development of the brain.

I can hear the cries of dismay from the anti-vaxxers already. Let me pre-empt them - its all a conspiracy, aliens control the world, blah-blah-blah...

Now, for reality:

The paper I'm referring to was published this week in Nature: Functional impact of global rare copy number variation in autism spectrum disorders. Nature, Published online 09 June 2010.

What this group did was take DNA samples from 996 individuals with autism, and 1287 people without autism, and screened their DNA for small mutations - changes in the number of copies of genes (called copy number variants - CNV's). What they found was, in some ways, not to surprizing - they confirmed that many of the genes tenativly identified in previous screens are in fact involved in autism; in addition they identified a few more genes - SHANK2, SYNGAP1, DLGAP2 and DDX53–PTCHD1.

As before, the genes they identified play a role in mediating the communication between neurons. In a previous post I described many of the previously known genes involved in autism. These previously identified genes fall into one of two categories - genes that regulate the communication between one neuron and the next, and genes that allow neurons to target damaged proteins for degradation. These newly identified genes all appear to fall into the first category - , SYNGAP1 for example, regulates the cycling of neurotransmitters.
But what this paper did that was really exceptional was a gene-function map - meaning they grouped the genes they identified into groups based on their biological function, and then mapped the relationships between those groups:

(click on image for full-size)

What we see in this gene map is the identified mutations fall into several broad categories, notably:

Cell movement - required for proper brain formation, and is required for neurons to make connections between each other - both during embryonic development.
GTPase/Ras signaling - required for the controlled release and recycling of neurotransmitters
CNS development - genes involved in forming our brains during embryonic development
Adhesion - allows neurons to bind to each other
Kinase activity - a set of signaling molecules that allow neurons to receive signals from the outside environment (hormones, for example) and respond to them. Required for proper brain development during embryogenesis.

The above tells us a lot about what is going on in the formation and functioning of autistic brains. But there is something key in the above data - notably, points 1,3 and 5. The fact signaling pathways required for brain development in embryos is involved is proof-positive that autism is caused not by vaccines, toxins, or other products of "big pharma", but rather is a genetically-encoded disorder that forms while the child develops in the womb.

The other cool thing here is that we now have the possibility of detecting autism early - potentially before birth, or at a minimum, immediately after. we know the sooner you start with specialized training, the better autistics do in terms of their neurological development. By identifying these individuals on the day we are born, we will be able to intervene early - hopefully helping them overcome some of the deficits they face sooner, rather than later, in their lives.

The cost of not vaccinating

2010-04-19T08:37:00.002-04:00

Anti-vaxers have been trying to convince people not to vaccinate their kids over a range of made-up concerns - vaccines have been claimed to cause everything from autism to spontaneous combustion. Of course, they don't, but that doesn't prevent the faithful from spreading their lies.

And once again, we see the cost of listening to these anti-vax loons. There is an on-going measles outbreak here in Canada; the first in something like 30 years, and guess who is being infected...

...100% of infections are in those who have not been vaccinated.

Yep, not taking those vaccines sure worked out well for these patients...

The reality is...

2010-04-16T09:22:00.000-04:00

Google is the closest thing to an omniscient entity in existence, which can be scientifically verified...

...and wikipedia runs a close second...

Great Vid

2010-04-15T12:46:00.002-04:00

Everyone should watch this:

EDIT:

And this one too:

How could you go wrong with a video where the speaker say "Pope Bennidect, I carry condoms all the time and I NEVER get laid".

I'll be chuckling about that one all day long!

Damage Control! What about moral actions instead?

2010-04-14T08:44:00.002-04:00

I'm sure everyone knows the catholic church is deeper into the shit than usual - a series of sexual abuse cases have broken across the world, revealing a systematic and widespread conspiracy by the church to hide paedophile priests from the law, and to ensure that the victems never recieve justice.

Needless to say, the discovery of decades of these sorts of cover-ups has - justifiably - pissed a lot of people off. And, as you'd expect, the church is in full-blown damage control. First they blamed the media, then it was the jews, now its the gays fault this occurred.

But notice whose not at fault - the catholic church itself. Yep, that's right, THEY hid the baby-rapers from justice, THEY moved the baby rapers around to avoid the law, but its NOT THEIR FAULT the baby rapers kept on a'rapin. Its pretty much everyones faults but their own - I'm surprised they didn't try to blame the victims themselves - that's probably next week excuse...

You'll also notice what is not forthcoming - either in the past or now - and that would be the only morally justifiable actions available to the church. Openness about their crimes and the crimes of their priests, and the turning over of all evidence and persons to the relevant police forces so that these criminals can be prosecuted.

Of course, those actions will never occur. This is, after all, a religion we are talking about here. For these organisations, moral actions always take a back seat to protecting ones organisation...

...now, if only politicians and the legal system would do the right thing, and declare the church a criminal organisation. It is, after all, what their coverup of crimes, and refusal to aid the police, makes them.

Hopefully not the last supper

2010-04-13T08:16:00.003-04:00

I love this image, courtesy of the Rational Crank. A far better group of heros for modern society could not be found:

(click image for full size)

The full list of who these esteemed persons are, and their contribution to society, can be found here. How many can you identify without help - I knew 11 of 13...

GOD IS REAL - at least, as of Wednesday

2010-03-25T09:15:00.002-04:00

Yep, you read the title right. As of Wednesday the Canadian John Paul LaPointe has had his name legally changed to God Dieux.

No magical powers though...

Another voice in the choir

2010-03-10T12:49:00.003-05:00

The science blogosphere has been afire the last day, all about an article analysing - of all things - science blogs. Most of the big names have waded in, and not being one to miss out on something popular (I jest) I thought I'd chime in...

Long article made short, this particular "study" criticised bloggers for:
1) Allowing too many comments,
2) Not keeping comments on track,
3) Occasionally being technical
4) Calling people names, and
5) Talking about more than one area of science - or even talking about stuff other than science

For example:

Science bloggers need to become more aware of their audience, welcome non-scientists, and focus on explanatory, interpretative, and critical modes of communication rather than on reporting and opinionating.

Basically, we're being criticised for not writing on-line textbooks and actually pretending that we're people instead of automatons. The blogs I linked to above take this paper to task; my view on it is much simpler.

Blogs are a means of personal communication - granted our audience is seldom known to use personally - but by-and-large blogs are vehicles for people to share their thoughts and opinions. The only thing that separates science blogs from other blogs is the fact that the authors of the science blogs talk, on occasion, about science. And, lie most people out there, we have interests that extend beyond our work. In many cases any education we pass onto our readers is a secondary consideration after our desire to simply share our thoughts.

If all I (or any of the more famous science bloggers out there) were after was to educate people, there are far better venues we could use. Blogs serve as a chance to share our opinions, and to discuss our ideas with others. Complaining our blogs aren't internet textbooks misses the whole point of blogging in the first place.

Are you an addict - better be religious then

2010-03-09T09:12:00.003-05:00

I like to believe that I live in a fairly advanced nation; one where everyone regardless of their faith - and even lack thereof - can receive treatment for their ails.

Turns out I was wrong - at least in Manitoba (one of Canada's provinces, if you didn't know). Turns out that their main addiction treatment program - and all 11 other programs they fund - offers ~~faith-based~~ "spiritual" treatment only. That's right - a government-funded health agency offers ~~religious~~ "spiritual", but not ~~non-religious~~ non-"spiritual" counselling to addicts.

Not only that, but the administrators of the program are completely unaware of what science has shown, and instead use a fallacy to support their fragrant violation of Canadian law:

Officials at the AFM remain resolute that recovery relies on at least some element of spiritual — but not necessarily religious — belief.

And just as a person's overall well-being depends on their physical health, it's the same for spiritual considerations, said Laura Goossen, director of the AFM's Winnipeg region.

Sorry, Laura, but that dog doesn't hunt. Comparisons of faith-based and non-faith based treatment regimens have been done and guess what - there's no advantage to including faith/spirituality when treating addicts. Study, after study, after study finds the same things - no added benefit to including faith/spirituality in addiction therapy program.

Or, in other words, Laura is speaking out of her ass. I find it amazing that a supposed expert in the area is completely unaware of the mountains of science demonstrating she is 100% wrong.

Of course, at least according to Rob Johnstone, an addict pressing a human right complaint against the Manitoba gov for their failiure to provide faith-free therapy, AFM does far more than include "spirituality" in their therapy:

[Johnstone] said he was encouraged by the AFM to find strength in God or a higher power in order to recover...And while in treatment at the latter program, he was approached to see if he was interested in attending services at a Christian church in Winnipeg

And if that were not enough - a gov-funded agency actively promoting religion, its turns out that Laura of the AFM isn't the only government official in Manitoba who lives under this delusion. According to an anonymous spokeswoman for the Manitoba gov:

A spokeswoman for Manitoba Health echoed the view that spirituality and treatment are inseparable..."Some degree of a spiritual component is common as these types of programs are believed to be more effective"

So there you have it - "blind faith" in the value of faith; a belief based on ignoring science being promoted by the government of Manitoba. I'm sure all the religious folks out there are dancing in the street - but the atheists, agnostics and unspiritual in Manitoba better hope they never need addiction counselling, because despite the evidence showing there is no benefit, the Manitoba government & health agencies are going to shove religion down your throats.

I wish Rob Johnstone, the Manitoba addict brining a complaint about this brazen abuse of government power to promote religion, all my best. May your complaint succeed, and may it force Manitoba to replace their faith-based program with one actually based on science.

The problem with petri dish science

2010-03-04T11:38:00.006-05:00

Over the past week a couple of the blogs I follow (Respectful Insolence for one, check it out) have been bloging about various topics like common lies told by animal "rights" activists and the shit-poor studies conducted by pseudosciences like homeopathy to make their work seem legit. One topic that has come up in these various blogs is the limitations of cultured cells - in particular immortalised cell lines - in scientific research.

This is of particular interest to be, because the current work I do involves extensive use of such cell lines, and prior to this I did my training in a lab where the rule of thumb was "if you cannot show it in an animal, it isn't real".

(above image - an image of a cell line [RAW264.7 macropahge])

To the uninitiated this may all seem a little odd, so to clarify I'll digress into the world of our bodies verses a petri dish. All of the cells in our bodies have a few general characteristics which is vital to our biology - they all maintain a relatively unaltered copy of our genome (mutations do happen in our cells, but are relatively rare), they all experience something called contact growth arrest (i.e. when they find themselves surrounded by other cells, they stop growing/dividing), they do not divide overly much (many do not divide at all) and they all require oxygen for their growth and function. The former three characteristics are central to preventing unwanted cell growth - i.e. cancer.

To make a cell line - basically cells we can grow ad infinitum in petri dishes, we have to overcome the third characteristic; little to no cell division. The ways this is done varries - you can frequently transfer the cells to new dishes, at low density, which stimulates their growth. Do this enough and the cells will eventually loose their ability to turn off their growth. You can also infect them with certain viruses, or derive your cells from a tumor. The only problem with these kinds of methods is they all greatly alter the biology of the cell. For example, getting the cells to divide faster reduces the time they have to check their DNA for errors, leading to accumulation of mutations and chromosomal abnormalities. For reasons not entierly clear, contact growth inhibition is also often lost when you overcome the growth defect.

The end result of this is that the cell lines we use - some of which were first derived in the 1950's - don't represent the tissues they are isolated from very well. Many take on full-on tumor characteristics - warburg respiration (i.e. they grow without oxygen), aneuplody (incorrect numbers of chromosomes), even regression to a more stem-cell like state (something common in tumours). In addition, they often loose protein expression of the very proteins that characterise the tissues they come from.

This has a real impact on science conducted using stem cells. Every day results generated using these kinds of cells are shown to be incorrect when primary cells (i.e. cells freshly isolated from the tissue) or animals/humans are used. That's not to say they are useless - 95% or so of what is discovered in cell lines holds true, but rather the results need to be taken with a grain of salt. And in many cases - particularity drug tests - cell lines cannot replicate the complexities of the mammalian body, including the inevitable metabolic processing of the drug - something which usually occurs in the cells of the liver, rather than the targeted cell/tissue.

This is of real importance when talking about the claims of animal rights activists, or pseudoscientists. For example, a common claim of animal rights groups is that animal studies can be replaced with these cell lines. This is wishful thinking on their part, both because these cells do not replicate the human body, nor do they even represent the tissues they were derived from. The same criticism needs to be kept in mind when talking to promoters of pseudoscience. For example, in this "study" woo-meisters test homeopathic remidies for cancer by comparing their effects on cell lines derived from actual tumours to cell lines derived from breast tissue (Orac demolishes the study here). The problem here (aside from the shit-poor "science" and lack of stats) should be obvious by this point in my post - those "non cancerous" cell lines are going to be close to, if not entierly, cancerous in nature due to what it takes to make a cell line. Regardless of how far along the road to cancer they are, one thing can be guaranteed - they're a long ways away from being real breast tissue.

The take home here is simple - cell lines are a powerful research tool. They've done more to uncover the inner workings of our cells than any other technique I can think of. But results generated in them need to be verified in primary cells or living organisms, and when using them in studies their limitations need to be forefront in our minds.

Good Advice - TAKE IT!!!

2010-03-03T12:40:00.003-05:00

Having just come from a conference I can say that every thing this guy says is true - most presentations are poorly designed and difficult to follow. This video explains how to make them better. To any scientists who happen by my blog - please follow this guys advice. I'm already re-vamping my presentations with his advice in mind:

Porn is good for you

2010-03-03T12:14:00.003-05:00

Science has some good news for any pornhounds that may be out there. Porn may be good for you.

Its long been though that porn is associated with a range of negative social attitudes; including promoting sexual violence and negative attitudes towards women. Turns out that, at least in the case of these two issues, this doesn't appear to be the case.

In a finding sure to piss off some feminists:

Now let’s look at attitudes towards women. Studies of men who had seen X-rated movies found that they were significantly more tolerant and accepting of women than those men who didn’t see those movies, and studies by other investigators—female as well as male—essentially found similarly that there was no detectable relationship between the amount of exposure to pornography and any measure of misogynist attitudes.

So apparently watching porn makes men less mysogynist, not more. It may even promote attitudes conducive to making for a long-lasting relationship.

Not only that, but viewing porn may actually act to prevent sex crimes. Quoting the article:

Over the years, many scientists have investigated the link between pornography (considered legal under the First Amendment in the United States unless judged “obscene”) and sex crimes and attitudes towards women. And in every region investigated, researchers have found that as pornography has increased in availability, sex crimes have either decreased or not increased.

So men, grab your...mice.

For a more technical review of the literature, click here.

Diamond, M. (2009). Pornography, public acceptance and sex related crime: A review International Journal of Law and Psychiatry, 32 (5), 304-314 DOI: 10.1016/j.ijlp.2009.06.004

Fingers Crossed

2010-03-03T08:33:00.005-05:00

As some of you may have noticed, we've gone through a bit of economic "trouble" over the past 2 years. Like most countries, my countries government spent billions of dollars trying to "stimulate" the economy; which as far as I'm concerned is a complete waste of money...

...but I digress. One thing that was interesting with these various stimulus plans is exactly what different govs around the world targeted with their stimulus dollars. The USA earmarked billions for scientific research, in the hopes of generating new technological products and stimulating green jobs. Here at home the opposite happened - funding to large scientific programs (Genome Canada, for one) was cut. Instead, our dollars went into building roads, and supporting largely foreign companies based in one province of Canada. This created an unusual divide - American researchers are flush with money; we Canadian researchers are scraping along on less than any time in recent history.

Well, it looks like the short-shifting of Canada's technological development may be coming to and end. Apparently, they have plans in the next budget to support R&D type work (which hopefully means more than restoring old funding levels).

Of course, we are talking about a government who's science & technology minister is a practitioner of woo (chiropractic "doctor") AND who is a creationist IDiot. So lets just say I don't have my hopes up too much.

The real irony, of course, is more money isn't nessisarily what we scientists want (although we wouldn't complain). Stable funding, or even a guaranteed minimal amount, would be a far greater gift - no more wondering just how much money there will be for the next round of grant applications, no lean year/rich year cycles, etc. But, as someone whose tried (and was stemmied by Canada's idiotic laws) to start his own biotech business what I really think they need to do is:

Provide some sort of tax breaks to capitalists and companies who invest in technology startups or who engage in R&D. As things currently stand, investing in R&D or new high-tech startups is pretty much a way of increasing your capital taxes. That doesn't exactly make these individuals want to invest in biotech startups, or engage in too much research of their own.
Reduce or simplify the business regulations. I shouldn't need to hire a law firm to simply start up a business - its almost as if existing business have bought out the political system to make it hard for new competitors to form...but that would never happen.
Take your hand out of the cookie jar. Recently, the gov's been passing laws trying to dictate where research funding should go. The only problem with that is that scientists are far more likely to be able to identify productive areas of research that the generally scientifically-illiterate politicians currently trying to pull the strings.
Send some of that stimulus money our way. You gave billions to foreign companies like GM (who also have spent a decade proving they are business failures); perhaps you could spread a little green to your fellow country men & women...

I'm hoping at least of of the above will come to be. But in the recesses of my heart I know that they'll fuck this one up; just like they've screwed up pretty much anything else.

This is worth repeatin

2010-02-26T10:12:00.000-05:00

Yes, its on every blog, but everyone should hear it.

Disease or variation?

2010-02-11T13:52:00.005-05:00

I've ended up in an interesting discussion on another blog (Dust in a Sunbeam by Optimus Primate, check him out), which through a serpentine route became the topic de jour at lunch today. Long argument made short, many of the diseases and conditions we previously thought were due to abnormal development are beginning - in some cases - to appear to be nothing more than the extremes of humanities evolution-derived biology.

Autism is the case that brought this up, and makes for a great example. Autism is a genetic disorder - there are literally dozens of genes that, if present in the right combinations of alleles, cause autism. But, these same genes appear in non-autistic individuals, and in some cases the "autism" alleles may actually lead to better intelligence, or greater artistic/mathmatic ability. Indeed, some of history's greatest scientists, artists & mathematicians may very well have been autistic (Einstein, Beethoven, Mozart, Yeats, Darwin and Turing as examples).

As we uncover more and more of autistic biology its beginning to look less like a disease, and more like a little piece of human evolution that is skewed in one direction. Autism is the genetic opposite of schizophrenia (i.e. "autistic" genes prevent schizophrenia, and vice-versa), and in many ways is also the behavioural opposite. As it turns out, the very genes that cause these two "diseases" are also those genes that appear to have changed while we humans developed our intelligence. The list of genes that cause these disorders reads like a list of neurological genes that changed as we evolved from our ape-like ancestors - FoxP3, Microcephalin, and so forth.

Likewise, as we learn more about these diseases the barrier between "disease" and "normal" grows faint. Aspergers patients (a "mild" form of autism) are often more intelligent than neuronormal individuals, appearing to many as super-shy individuals and nothing more. And their "normal" parents often score below "normal" on many of the tests used to ID autistics. The same is true of schizophrenia; between the "disease" and "normal" is a huge range of people, exhibiting behaviours that while odd are a far cry from being a disease.

The net effect of this is that these "diseases" may not be diseases in the classical sense of the term, and instead simply represent the "tails" of normal human variation. This, in my mind, brings up a couple of serious ethical questions. And as our understanding of the causes of these "diseases" increase, they are questions we will need to seriously consider before developing therapies:

Is it right to treat part of normal human variability as a disease?
Are the symptoms of these individuals truly something we need to intercede with? (This is an especially thorny question when talking about individuals on the "mild" end of the spectrum).
Do we have the "right" to label genetic variation as a disease, and the "right" to mess with it?

Autism puts these questions into stark contrast. We now know that many of the genes mutated in autistics are the very genes that mutated to give rise to human intelligence. We know, based on the "symptoms" of autistics, that these genes have an important role in determining how our brains work. We also know that some of these genes, when put together into the right combination, lead to amazing leaps in intelligence - savantism for example. Likewise, we know that many of these genes are actively evolving today.

These question may seem philosophical in nature - what "right" do we have to tell someone they are diseased, etc. But we are on the cusp of being able to alter our own genetics, and when that day comes this issue will be propelled from a philisophical issue to one which is very pertinent. We don't know why the genes that cause autism (or schizophrenia) have been maintained by evolution. We don't know if these variants are important in maintaining human intelligence. And we have no idea what future role they will play in the humankinds ongoing evolutionary story. Any treatment for autism could very well quell the next step in the evolution of the human brain.

Its a sharp knife - on one side we have the health and well being of people to worry about; but on the other side of the blade could very well lie humanities future.

Its g-g-g-genetic

2010-02-11T09:46:00.006-05:00

Pardon the title, but in somewhat shocking news (to me, anyways), it turns out stuttering is genetic. A study released today in the New England Journal of Medicine has identified mutations in two genes - GNPTAB and GNPT - that seem to cause stuttering. These mutations seem to be found in stutterers around the world, although the initial mutations were identified in a Pakistani family.

The real odd thing though is what these genes do - they're involved in sending proteins to lysosomes; our cells version of a garbage bin. Lysosomes are nasty places, where parts of our cells go to die - they're acidic, full of oxidents, and full of enzymes whose sole job is to destroy anything that fall into their maw.

Genetic diseases involving lysosomes are somewhat common, and while the exact symptoms vary depending on the gene(s) which are mutated, they all have a common thread - neurological problems. In fact, most of these disorders have profound - often lethal - effects on a patients neurology. So in some ways the link between stuttering and lysosomes makes sense - lysosomal mutations often have neurological outcomes. But the mildness, and limited affected area (speach, not much else) in this case is very, very odd.

So what exactly does GNPTAB and GNPT do? Turns out both are pieces of a large complex whose job is to tag proteins that need to be sent to lysosomes. This tag is a sugar (GlcNAc), and acts as a sorting signal that tells our body "this protein should go to a lysosome". Proteins tagged in this way are generally not being sent to lysosomes for degradation, but rather are the active components of lysosomes. So mutations in these genes should make for less active lysosomes, which in turn may lead to the buildup of damaged cell components in affected individuals.

How and why these mutations lead to stuttering remains a mystery. In fact, other mutations in GNPTAB are known to cause two severe disorders called "mucolipidosistypes II and III"; disorders which cause sever cardiac, skeletal and eye issues. The fact that these mutations seem to selectively affect one region of the brain (presumably the speech centre) is particularity hard to explain, given the diverse effects of other mutations in the same gene.

Whether or not this discovery does anything to help stutterers is an open question - although it does get overbearing teachers and parents off the hook.

Kang, C., Riazuddin, S., Mundorff, J., Krasnewich, D., Friedman, P., Mullikin, J., & Drayna, D. (2010). Mutations in the Lysosomal Enzyme-Targeting Pathway and Persistent Stuttering New England Journal of Medicine DOI: 10.1056/NEJMoa0902630

Arthritis, platelets, and inflammation

2010-02-02T11:46:00.005-05:00

As I mentioned in my last post, this has been a watershed week in two areas I'm greatly interested in. Two major discoveries were published last week that are in areas of great interest for myself. My first post concentrated on one of my favourite parts of the cell - mitochondria. The second article I want to blog about is a blast from my past, and involves inflammation - the major way our immune system gets rid of bacteria, and ironically, the cause of many human diseases.

This paper discusses the role platelets - the miniature cells that help our blood clot - play in making some forms of arthritis worse. It also addresses the role of a biological mystery - microparticles - play in mediating disease.

Platelets main role is to form blood clots - upon breaking a blood vessel they encounter the proteins that "glue" our cells together. Upon identifying these proteins (and protein products formed when this "glue" is exposed to blood) platelets glom together, forming a clot. At the same time they release chemical signals that inform our bodies that the blood vessel is damaged and that an immune response is needed. In many cases those chemical signals are the first warnings our immune system has that something is wrong. But in a few cases damage caused by the immune system results in platelet activation, in which case those chemicals tend to aggravate the underlying condition.

The second half of this story surrounds microparticles (image at left) - microscopic sized fragments of cells that are found in the various fluid of our bodies. Even today the source, cause and purpose of these particles remains elusive. Whether they're deliberate products that have an evolutionarily-derived purpose, or whether they're an abnormality caused by biological malfunction, is not known. A large range of cells are known to produce these particles, but in only a small number of cases do we know how, and why, these are made.

The authors of this paper have tested a couple of fairly simply hypotheses - do plateltes form microparticles during an inflammatory disease (arthritis), and do those microparticles alter the disease itself?

The answer to the former question is a resounding 'yes'; the number of platelet-derived microparticles increases by a huge amount during arthritis. Not only that, but the researchers were able to determine that one single receptor - the collagen receptor GPVI. Collagen, by the way, is one of the glues which hold our cells together. By blocking the interaction of GPVI with collagen this group was able to both stop microparticle generation, and reduce the severity of arthritis. The image to the left shows a platelet releasing microparticles.

Which leads us to the second question they asked - do these microparitcles affect the disease? Obviously the answer is 'yes', as removing the particles reduced the severity of the disease. Exactly how this occurs is a bit of a mystery - although we know a chemical signal called "interleukin-1" is involved.

What this means for patients is twofold - first of all, it validates the idea that the presence of these microparticles may be a way to detect disease. Emphasis on the "may" - we simply do not know enough about these particles to really make any firm predictions at this point. The second thing this does for patients is open the door to new therapies, targeting either GPVI or the microparticles themselves.

Boilard E, Nigrovic PA, Larabee K, Watts GF, Coblyn JS, Weinblatt ME, Massarotti EM, Remold-O'Donnell E, Farndale RW, Ware J, & Lee DM (2010). Platelets amplify inflammation in arthritis via collagen-dependent microparticle production. Science (New York, N.Y.), 327 (5965), 580-3 PMID: 20110505

The cause of Parkinsons?

2010-02-02T11:14:00.007-05:00

One of the more frustrating things about being a scientist is we often spend weeks, even months, between discovering (or reading about discoveries) that make a real impact in fields we're interested in. The last week was far from a frustrating week, in fact large advances were made in two areas I'm interested in (plus a bunch of cool stuff in other area's, like figuring out the colouration of some dinosaurs). Weeks like this are rare, so I'm dedicating the next two posts simply to what happened last week.

This post is on an amazing discovery in regards to Parkinsons disease, a degenerative neurological disease that affects many of the elderly. Parkinsons itself has been known to be partially a defect in mitochondria - the energy-generating parts of our cells. For reasons that are still a mystery, the buildup of broken mitochondria leads to neurodegenerative diseases like Parkinsons. We've known for a long time that Parkinsons is partially genetic, and a few genes have been identified as culprits. Two in particular have been known to be major players and - PINK1 and Parkin. But while these two genes have been known to be important for a while, exactly what they did to cause Parkinsons disease was unknown - until last week.

As it turns out these two genes play a role in regulating the removal of damaged mitochondria. PINK1 has been known to be stuck to mitochondria, where it is though to phosphorylate proteins on mitochondria that are no longer functioning properly. For those of you who are not bio majors, phosphoryaltion simply attaches a little chemical tag to a protein. That tag can be recognised by other proteins, or can modify the activity of the tagged protein itself. Exactly what that tag did, in terms of getting rid of damaged mitochondria, has long been a mystery.

As it turns out the purpose of that tag is to bring in another protein, called Parkin, to the mitochondria. As odd as it may seem, Parkin's job is to attach another kind of tag onto proteins - a tag called "ubiquitin" (picture to right). On the surface tagging a tag may seem a little redundant, at least it does until you realise that ubiquitin is a very special kind of tag - ubiquitin is usually used by our cells to tag things for destruction. So PARK1 and Parkin act as a team; PARK1 sits on mitochondria and acts as a sensor. When PARK1 detects that a mitochondria is not functioning properly it phosphorylates (tags) the mitochondria. This tag brings in Parkin which then adds the final tag that leads to the destruction of the defective mitochondria, through a process called autophagy (literally "self-eating).

You'd think that figuring out how these proteins work would be enough to make a scientist happy - but no, this group had to take things a little further. Not only did they discover how these two genes act to destroy defective mitochondria (and thus prevent Parkinsons), but they also showed that the mutations in these genes most often found in people with Parkinsons prevent this process from occurring.

What is really exciting is what this potentially offers for patients. At the very least this discovery may lead to genetic tests that would allow us to detect potential Parkinsons patients decades before they become symptomatic - perhaps allowing us to treat the disease before it happens. But it also opens up the door to other options - new drug regimens, gene therapies, even stem cell therapies, to treat - or even better - prevent Parkinsons.

Geisler S, Holmström KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, & Springer W (2010). PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nature cell biology, 12 (2), 119-31 PMID: 20098416

Ignorance in the Name of Jesus?

2010-02-02T10:47:00.000-05:00

I often fall into conflict with my fellow atheists over evangelicalism; not religious evangelicalism, but rather the atheistic version thereof - actively converting followers of irrational religious belief's to the rational beliefs of atheism. Many of my brethren strongly believe that we should be out there, spreading the good word (so to speak). I disagree, not because I don't believe that rationality isn't worth fighting for, but rather because such activities act to propagate the very thing that religious faith depends on...

...Ignorance

The worlds various religions, in their various forms, did their best - and continue to do their best - to keep their flocks ignorant. Indeed, a dark, scary, unintelligible word has room in it for demons, angels and god(s). The problem, from religions perspective, is that every time humanity learns something new we push back the darkness a little bit, leaving a little less room for the supernatural, and thus leave a little less room for religion. Not too surprisingly, most religions try very hard to keep that curtain from being pushed back.

The Christian church, in its various flavours, are a perfect example of this. For over a millenia the Christian church operated solely in latin. By that time Latin was a dead language, and thus the church deprived most of its members of even a basic understanding of their own faith - including the contradictions and outright evil acts of god . The exemption on keeping faith latin was absolute - translation of the bible or providing mass in any language other than latin was strictly forbidden, oft on the pain of death.

It took over a millennia, but this eventually began to change - first mass and with bibles were translated into local language. But even that slight lifting of the darkness - simply allowing people to know their own faith - did not come easy. In many ways the war wasn't won until the 1450's, with Gutenberg's invention of movable type, which move duplication of the bible from the world of religious scribes to the world of the educated gentry. Finally, nearly 1400 years after it was written, the bible became a book of the masses.

But the promotion of ignorance didn't begin, or end, with the bible. The litany of those persecuted and murdered by the church, for simply thinking thoughts outside of 'god is good', is beyond repetition. We will never know the toll that was extolled, other than a few cases where the very brightest of humanity was stamped out by the darkness of catholism. Some, like Galileo and Da Vinci got off easy - they were simply threatened with torture and death if the continued to pursue certain lines of thought. Others were not so lucky...

...One of the more unlucky, and yet amazingly percipient, victims of the church was a little-known man by the name of Giodano Bruno. Bruno was a philosopher, scientist and mathematician. Born just a few years after Copernicus "discovered" the true nature of planetary orbits, and decades before Galileo proved Copernicus to be correct, Bruno hit upon a simple truth that wasn't rediscovered for centuries:

Our sun is but one star among many, the family of planets circling our star are but just one family of many orbiting other stars. He even went so far as to propose life may exist on other planets, and to contemplate on the nature of god.

His prize for discovering a few simple truths - the church nailed his tongue to his jawbone, and then burned him alive.

As time went on this kind of retribution became less and less common, as the church began taking other route to keeping their flocks ignorant. When the church couldn't suppress translations of the bible, they tried to limit the education of the masses. When that failed, they tried to limit education to men (something which sadly still occurs in some ways in the western world today).

Fast-forward to today and you can see this policy in action - the church cannot murder those who study the universe and the myriad ways in which it works. They cannot murder the publishers who disseminate these materials, nor the teachers who pass the information onto their pupils. Instead, they now target the pupils themselves - the oppose, and try to limit, the teaching of nearly every branch of science - evolution, geology, palaeontology, genetics, cosmology and so forth all provide an explanation of the universe that runs contrary to the bronze-age creation myth to which the subscribe.

They demonize those who would uncover and teach these truths - scientists, teachers, even fellow members of the clergy who find science to be "cool". And these actions are not limited to a small number of extremist churches; even the more "liberal" churches maintain lists - formal or otherwise - of books, movies, etc, that they would prefer their members not see. They "instruct" their followers on how to incorporate science into their religious view point, and so forth.

The above seems to be quite off-topic to how I started this post, but trust me, there is some relevance. The point of the above rant was simply this - religion feeds on, indeed subsists on, ignorance. When ignorance is replaced with knowledge, religion looses ground. Every step towards intellectual enlightenment is a step backwards for god(s).

By seeking converts atheists would be playing the same game - simply asking people to exchange one belief for another. If successful such an evangelical path would simply create a host of unbelievers who became atheists simply because someone told them to.

I cannot speak for all atheists, but I know many came to their beliefs through the same route I did - through introspection, thinking about ones beliefs, and inquiry into my religion, other religions, science, philosophy and the world in general. Through this path - learning - I came to understand the simple truth that religion is a human construct, as are our gods.

As atheists we should be promoting this path - learning, education and introspection. Only through that approach will we truly free the world of the parasite of religion. To convert is simply to continue on as per usual - belief without knowledge, ignorance in exchange for intelligence. By seeking converts we would cast down a repressive pathos of faith and replace it with a repressive pathos of atheism.

This shouldn't be our goal, we should try to be better than the religions we oppose. Instead of conversion we should seek education, free thought, rationality, and equality. Only through such a route will we be able to rout the ignorance - both religious and secular - that permeates our society. By replacing ignorance with knowledge and rationality we will achieve the world we want - one where rationality and fact rule, and where irrationality, fear and sciolism are regaled to the dustbin of history.

Religion, in all its forms - pantheistic, monotheistic, even atheistic - would not survive in such a society. The religious mode of thought - beliefs out of fear, ignorance and conformity - would fall. The impact of this would extend far beyond simple religious beliefs - politics, business, even day-to-day interactions between people would change, and all for the better.

RIP, or the little robot that could...

2010-01-29T10:05:00.001-05:00

Game changer

2010-01-27T11:48:00.004-05:00

I'll apologise now for the geek-out, but sometimes a little piece of science comes around that sets my nerd-senses tingling. One such event happened a few days ago, and I'm still working it into my world view - this is a game changer (at least in the little corner of the scientific world in which I live. Sorry, but I need to yell for a second:

INTEGRINS CAN ENGAGE G-PROTEINS!!!!!!!

Not impressed? You should be - unless, of course, you don't know what integrins or g-proteins are.

As per usual, some background first.
Cells need to stick to things, otherwise we wouldn't exist - instead of a person reading this, you'd be a blob of gelatinous goo if your cells didn't stick together. One of the more important molecules that does this is called an integrin (image to right). What makes these special is that they can be turned on/off (called inside-out signalilng), and they also let the cell know if they have bound to something (called outside-in signaling).

G Proteins are something else - they are a family of proteins used by our cells to transmit signals. In the case of this study the particular G-protein involved is one that normally binds to "G-Protein Coupled Receptors", which are the most common type of receptor used by our bodies to respond and detect stimuli. Your immune system uses them to respond to some kinds of bacterial products, they're what allow for you to taste, feel, smell and see. They allow your nerves to work, your blood pressure to change, and they let your blood clot when you get a cut.

So what is so amazing about integrins interacting with G-Proteins? Its amazing because this shouldn't happen - numerous signalling molecules have been implicated in integrin signalling, but nothing that looks like a G-Protein. Likewise, G-proteins are not known to interact with anything other than a G-Protein coupled receptor.

OK, that was a lot of background, so what did these guys discover?

As I mentioned above, integrins are involved in the clotting of our blood. One integrin in particular - alphaIIb beta3 - helps hold those clots together. Later, once the wounds has healed, the platelets in the clot use the same integrin to controct the clot, thus re-opening the blood vessel to blood flow. In platelets floating around in your blood this integrin is usually turned off - it won't stick.
But when our blood clots a protein called thrombin is activated, and in turn activates on of those G-Protein Coupled Receptors I mentioned above, which in turn activates a G-protein.

Once active, that G-protein moves around the cell, turning on and off various biological processes needed to make a clot. Here is the first amazing thing this study found - one of the things that gets turned on is alphaIIb beta3, by directly interacting with the G-protein. This allows the platelet to bind the clot. The second amazing thing occurs later on - when the integrin binds to the clot it re-activates the G-protein; sending a signal into the cell which causes the platelet to contract.

OK, so maybe that's not as exciting as it originally seemed, but I did that kinda work back during my PhD - but I didn't get into science...

Gong H, Shen B, Flevaris P, Chow C, Lam SC, Voyno-Yasenetskaya TA, Kozasa T, & Du X (2010). G protein subunit Galpha13 binds to integrin alphaIIbbeta3 and mediates integrin "outside-in" signaling. Science (New York, N.Y.), 327 (5963), 340-3 PMID: 20075254

Evolving Robots

2010-01-27T10:54:00.004-05:00

Creationists often like to claim that complex traits cannot arise from the "simple" processes of mutation and selection. They often claim that these processed are not even observable (even though we've been observing them since we began breeding plants and animals).

Anyone with even a basic grasp of science knows the above claims are pure BS, but not being content with simply being right, some scientists have now gone the extra mile and used evolution to make ROBOTS.

And not just any robots - robots that walk, hunt each other, evolve their shape, and which are even altruistic - a distinctly mammalian trait. All of that was evolved; starting with nothing more than a collection of parts and a simple mutation/selection algorith.
The above image shows one such robot - in this case, this is an example of a walking robot whose shape evolved through autonomous design and fabrication. Fancy way of saying the parts were randomly put together, mutated, and selected until a functioning robot was formed.

Pretty freakin' cool if you ask me!

This is hardly the first time computers and robots have been used in evolutionary experiments. but what does make this experiment unique is that its the first time evolution of structure and evolution of behaviour have been done in one experiment. In the past groups would either have a set structure whose behaviours evolved, or a pre-set series of behaviours that a object was then evolved to fit.

So what does this actually teach us about evolution? Especially given the very simple evolutionary algorithm the used (see above image) - an algorithm far simpler than the "algorithm" of biological evolution.

As it turns out, this study teaches us a lot about evolution, notably:

Small mutations can lead to very rapid changes in form/behaviour. All of the behaviours appeared quite quickly in these experiments - usually a functioning behaviour/structure would appear in a few dozen generations, and after 100 or so generations the behaviour/structure would be highly defined.
Once a behaviour/trait is formed, it is optimised very rapidly.
Very simple systems (in this case consisting of a few hundred parts - compared to the thousands to tens-of-thousands of genes in living organisms) can be moulded by evolution into extremely complex beings, capable of complex - even cooperative - behaviours.

But we all know what the creationist response will be - "but its still a robot". Yep; they started with random collections of parts that couldn't do anything, evolved them into walking, hunting, cooperating robots, but that couldn't possibly be evolution...

Floreano, D., & Keller, L. (2010). Evolution of Adaptive Behaviour in Robots by Means of Darwinian Selection PLoS Biology, 8 (1) DOI: 10.1371/journal.pbio.1000292

But is it ethical?

2010-01-25T11:31:00.001-05:00

As the small numbers of followers I have know, I am deeply opposed to all of the pseudo-scientific (why do we call it that? pseudo suggests that its similar to, or appears like, science. It doesn't. Anti-scientific, anti-rational, pro-stupid would all be better terms).

I digress. I am deeply opposed to all of the psuedoscience quackery out there - be it naturalpathetic "medicine", CAM, homeopathy, creationism, anti-vax lunacy, and so forth.

But I also have to live in this world, and part of this world is paying the bills. This hasn't been an issue to date, but the wife and I are looking at having a child soon, and buying a house. Needless to say, we need more cash, and we need it quick.

I've been hawking my skills as a technical writer (I know, my blog doesn't read like I have a grasp of the English language, but I can be quite literate when I need to be), and my wife has been looking for additional lab-tech type work.

Recently, she applied to a quackfest of tomfoolery. To protect the guilty (i.e. her potential future employers) I won't say who/what they are/do, but needless to say its about as scientifically valid as flat-earthism.

Which raises an ethical dilemma: is it ethical for a rational, intelligent person to knowingly work for a company whose product/service preys off of those who are neither rational or intelligent?

I guess what I'm asking is if it is OK to fleece stupid people?

I'm on the fence - I feel that I should support science and rationality in all aspects of my life. But then again, stupid is as stupid does, and money from stupid people is just as green as money from intelligent people (and damned easier to get). My wife falls on the side of "who gives a f__k, we need the money".

I think my wife holds the correct position...

A picture is worth a thousand words

2010-01-20T14:00:00.002-05:00

'uff said.

From: http://www.creators.com/

Evolution of morality

2010-01-14T15:32:00.000-05:00

A common argument (or perhaps comment would be a better term) is that atheists cannot have morality, based on the fact that we have no god(s) to give it to use. This, of course, is bupkis.

Ignore, for a second, the fact that all good parents teach their kids moral behaviour, and that society demands moral behaviour of us. And while you're at it, ignore the numerous religions that either a) have no god(s), b) have god(s) as fallible as humans, or c) have a god and yet are the basis of much immorality.

OK, the last one is ALL religions, but I digress.

Aside from the obvious illogic of the claim that you need to believe in god to be moral, there is a clear and concise answer as to why it is wrong - evolution.

Humans are what we scientists refer to as a social species - that is, a species that lives and functions largely as groups, rather than as individuals. We are hardly unique in this - wolves, dogs, deer, chimps & other apes, dolphins & most whales, ants, termites, bees, horses, cows, sheep, goats, many kinds of birds, etc, are all examples of social species.

Organisms gain great evolutionary benefit from working as a social species - be it in the form of protection (a herd of deer is much safer against predators than is a lone animal), increased capture of food (wolf packs can take down large prey, single wolves are usually limited to small animals), sharing of resources, sharing of caring for the young, grooming to prevent disease, and so forth.

But not just any species can behave in a social manner - a species needs to evolve a series of traits - AKA morality - in order to function as a social species. Without a "code of ethics" no social species can survive. And the base of most/all human ethical systems can be seen in our social animal brethren.

Take for example, violent behaviour against others in your social group (herd, pack, tribe, workplace, etc). This behaviour harms the group, by impairing or removing members of it. This in turn costs the individuals in the group - both the individual(s) harmed by the violent behaviour, but everyone else as well (due to varying costs; decreased food acquisition, or the burden of caring for the injured). Not too surprisingly, most social species have a strong bias against such behaviours.

The same can be seen in the cases of most of our moral behaviour - sharing resources without immediate payback (altruism) is common among all social animals. Likewise, most social animals have the golden rule built-in (reciprocity, i.e. treating others well, in the expectation they treat you well as well) and a built-in punishment system for violations (usually ostritization or expulsion from the group).

Strange - despite not having gods, religions or bibles, animals have managed to come up with morality...

Now, given the apparent evolutionary basis for morality one would expect there to be a morality gene of some sort. That's not entierly true - behavioural traits are almost always the product of multiple genes working together, and often involve disparate genes such as those responsible for brain structure, neuronal interconnectivity and hormonal levels.

None-the-less, morality genes have been identified, mostly in animals. But at least one morality gene has been identified in humans - specifically monoamine oxidase, which when functioning normally prevents us humans from committing violent acts against each other. Individuals carrying mutations in this gene are more likely to engage in violent behaviour. Monoamine oxidase, when working properly, regulates violent behaviours by breaking down neurotransmitters.

As it turns out, there are a lot of mutations in monoamine oxidase, spread throughout the human population. Exactly how all of these impact on our social behaviour is a bit of a mystery, but luckily its only a minor subset of those mutations that cause violent behaviour.

There is obviously a long ways to go until we understand the entirety of the biological basis for morality. There are still many uncertainties as to how learned behaviour can compliment, enhance or counter our innate (genetic) morality. Likewise, its unclear how much of these traits are uniquely evolved in humans (probably little-to-none), inherited from our ape ancestors (probably a goodly portion), or inherited from much more distant ancestors (probably a goodly portion as well).

And while there are a lot of open questions, on thing is clear - morality is not some magical pie-in-the-sky-gift-from-god. Its as much a part of our evolutionarily-inherited biology as the colour of our eyes, or our pancreas.

Sometimes environmentalists piss me off

2010-01-12T14:04:00.000-05:00

I consider myself to be an environmentalist - I do my best to reduce my environmental impact, volunteer with projects aimed at restoring damaged habitats, walk to work, own a fuel efficient car, and so forth. Almost always, I come out on the side of of the "greenies" in arguments.

But sometimes I wonder if the ranks of my fellow environmentalists are filled with idiots...

A recent issue, both here at home and more recently at Stockholm, is my countries tar sands. For those of you not-in-the-know, the tar sands are the newest source of oil, and consists of tar-soaked sand. The sand is strip-mined, and the tar removed by heating the sand. The tar can then be processed into crude oil and other oil products.

This process is messy - there are the usual run-off issues that come with mine tailings, the strip mining destroys local habitat, and the high degree of processing needed to convert tar into usable fuel consumes a large amount of energy. Because it is such a large and obvious target, many environmental groups have targeted the oil sands, in an attempt to get them shut down.

That is, simply put, stupid. Despite the dirtiness of it, oil sands account for ~1% of Canadian CO2 emissions (which, in turn, account for about 2% of global totals). So eliminating the tar sands wouldn't exactly put a big dint in Canada's CO2 output, and wouldn't even be noticeable on a global scale. Further more, the impact would be even less than 1%, as the tar sands would have to be replaced with another source of energy.

In contrast, transportation accounts for about 20% of GHG's in Canada, as does generating electricity. You could get an equivalent cut in CO2 simply by raising fuel efficiency or electrical generating efficiencies by 5%.

So while the oil sands make for good media optics, they are all but meaningless in terms of making significant environmental impacts.

A better option would be to push for broad-spectrum changes - industrial caps, increased fuel economy standards, improved building standards, etc. Small increases in efficiencies, spread throughout industry and society, would create large decreases in total GHG production. Supporting mitigation procedures - GHG capture, planting new forests, and other forms of carbon sequestration - could also go a long ways. Likewise, beginning to move our energy base towards low-CO2 (i.e. natural gas, biogas/biofuel, etc) and no-CO2 (nuclear, wind, hydro, solar, etc) would also have a tremendous impact.

But instead the greenies focus all their energies on a minor, albeit ugly, player.

I guess it goes to show that some people prefer appearances over actually doing something. I proudly place myself in the latter category - its unfortunate that so many of my fellow greenies place themselves in the former.

The vatican is at it...again

2010-01-12T12:25:00.000-05:00

So once again the pope (or at least his representatives) has opened his mouth, and as per usual nothing but nonsense came out. At least this time no one should die...

So guess what the pope is pissed about now...a movie. And not even a Da Vinci code, "the church is evil" kinda movie. Rather, he's mad about Avatar, an animated film with an underlying environmental theme. His problem - apparently the movie treats nature as a little too spiritual for his liking. Instead of treating nature as a gift from the magical sky fairy - something for us to use or destroy as we wish - "avatar" instead treated nature as something delicate, something to be protected.

Yep, that's a bad thing according to el pope-o. Leads to "neo-paganism", which I think is priest-speak for "giving a shit about something other than filling the churches ~~pews~~ coffers".

Grab your pitchfork - time to burn some movie directors...

One law for you, one law for me

2010-01-06T15:29:00.001-05:00

I doubt there are many western democracies where the general citizenship would agree with the statement "everyone in my country is treated equally by the legal system". We all know that those who have money get to purchase justice, in the form of effective legal teams, convoluted (and often long) legal proceedings, and appeal after appeal after appeal. Even if they're eventually found guilty, their dead by the time everything works its way through the courts.

The rest of us get the shitty end of the stick - self-representation, or if we're "lucky" a ~~newly graduated, inexperienced, ineffective and outclassed shitbag of an excuse for a lawyer~~ public-defence lawyer.

Nor would many people disagree with the statement "celebrities, politicians and other public individuals get treated more mildly by the legal system than the rest of us".

And just to show that my own country is just like everyone else's, our darling legal system just let a guy by the name of Eric Tillman (pic @ right) off the hook - AFTER HE PLEAD GUILTY TO SEXUALLY ASSAULTING A 16 YEAR-OLD GIRL. Yep, he plead guilty and his debt to society was...nothing. No jail time, no parole, no fine, not even a criminal record.

And the judges reason why - and I jest not:

Judge Murray Hinds told a Regina courtroom Tuesday he believed Tillman was "genuinely remorseful" for his behaviour.
"In this case there's no suggestion that Mr. Tillman is not generally of good character," Hinds said.

"He has no prior criminal record. His behaviour towards (the teenage girl) on Aug. 6 appears to be an aberration fuelled by his consumption of two non-prescription drugs, which he used for sleep and pain relief."

Of course, the fact that Tillman is the GM of one of Canada's major football teams, is very wealthy, and is a public figure played no role in that...

...oh wait, it did. According to Tillmas lawyer one of the arguments used to secure his generous treatment was the fact that as a public figure Tillman and his family will face ostracization by the rest of society.

GASP - how horrendous; a child molester being ostracised by society. What's next, imprisoning murderers? I do believe the sky is falling...

Gee, I wish I was rich and famous - I could commit any number of crimes, and then afford a scum-bag lawyer who'd get me off because I'm famous and therefore people might not like me.

Instead, I'm going to have to choose option 'B', and not commit any crimes...

I'm not a fan, but...

2010-01-06T13:31:00.000-05:00

I'll admit to not being much of a fan of the Sea Sheperds. For those of you unfamiliar with this group, they're an environmental group whose aim is to end whaling. While their goal is laudable (and one I support whole-heartedly), their tactics are not. Unlike Greenpeace and other organisations, who function primarily through documenting whaling activities and raising public knowledge, the Sea Shepherds use a variety of "direct-action" methods designed to interfere with whaling operations.

These tactics fall into a grey area, in terms of international law, and there have been a few incidents where they appear to have deliberately damaged ships at sea - an activity which is against numerous international agreements, activities which potentially puts human lives at stake, and an activity considered to be a criminal offence in most nations. Some have suggested that their activities may even push into the realm of terrorism, given that they have been linked to a few attempts to sink whalers using mines.

Furthermore, it is my opinion that these activities most likely function to help whalers by undermining any public opinion that is built up against whalers. After all, these activities taint anti-whaling advocacy with more than a hint of extremism.

All the above said, the Japanese have crossed a line, and crossed it in an extreme way. About 12 hours ago they deliberatly rammed and sunk a small Sea Sheperd speedboat. No reports of fatalities, but its a serious and illegal activity none-the less. The first video that was available can be seen below, and was provided by the Japanese whaling fleet:

There's a couple of ways this can be interpreted:

The Japanese were overtaking a slow/non-moving vessel and failed to give-way. Under international maritime rules this is a big no-no, as overtaking vessels are required to ensure they pass the other vessel safely, and the overtaking vessel is required to change their course appropriately.
The Japanese and sea shepherd vessel were on a cross-course. In this case the vessel which has the other vessel on starboard must give way. The sea shepherd vessel is clearly on the right (starboard) side of the Japanese vessel, once again meaning the Japanese should have given way.
Some people claim that the sea shephard vessel accelerated towards the Japanese vessel immediately before the collision. Even if true, it doesn't change the fact the Japanese failed to follow maritime law, as outlined in points 1 & 2.

The sea sheppard have now released their own video (see below). This one is much more damning for the Japanese, as it shows that the Japanese vessel clearly turned TOWARDS the sea sheppard ship. This is a gross violation of international maritime law, and likely constitutes a criminal act in nearly every nation on earth.

So while I don't like the way the sea sheppards do their thing, I hope that this incident is sufficient to bring a criminal case against the Japanese whaling fleet. With luck this incident will either force nations to stop the hunt, or at least give sufficient grounds to sue the Japanese fleet into insolvency.

Do you boinc?

2010-01-05T10:50:00.000-05:00

If you're looking at this you own a computer (or at least are borrowing one from someone). Did you know that the average persons computer spends most of its time idle - millions of unused clock cycles disappear between each and every keystroke and mouse click you make.

That is a huge waste.

We scientists often need a huge amount of computing power - I preform image analysis routines which often take 2 days of solid computing (on a 16-core machine) to complete - and on the scale of things I'm a light user.

Now of only there were a way to use all of your unused clock cycles to help out people like me.

Boinc is the answer. Developed by the people at SETI, but used by many high-computing needs research groups, boinc allows individuals like yourself to donate unused clock cycles towards scientific projects. There are dozens of projects you can donate your computer cycles to - want to help find aliens, link up to seti@home. Want to help predict the future climate of our planet, link upto climate prediction. Want to help reveal the inner world of the cell - link upto Rosetta.

And there are dozens more to choose from, covering every scientific discipline out there.

I boinc - SETI@Home and Rosetta. You should too.

Research Blogging is finally working

2009-12-30T14:38:00.000-05:00

I joined research blogging in the hopes of attracting more attention to my blog. But for nearly a month, none of the posts I tagged were appearing in research blogging. I finally resolved my issue, and for the sake of others who may encounter this issue, here is my solution.

The problem lies with the way blogger handles custom-entered HTML. Basically, a critical part of the HTML needed by RB gets stripped. To fix this, AFTER posting your post, re-edit it in HTML mode. Within the RB citation find every "< span" and add "class="Z3988"" after it.

Oh, and there is no space between '<' and "span", but blogger won't even let me type that...

Simple fix, but it would be nice if blogger would not edit HTML I enter myself

Alt Med fails again

2009-12-30T09:31:00.000-05:00

Some of you may have heard of this "alternative medicine" fad going around (OK, its been going around for centuries, although we used to call it things like witchcraft, and snake-oil). And despite its name, it is not medicine. Out of the thousands of alt med products out there, there is a tiny handful (3, as of my last count) that actually have clinically measurable benfitits.

Today we're NOT adding another to that list. For decades (perhaps centuries) people have been claiming that Ginko biloba helps your brain work. Its been touted as a cure for everything from insanity, to ADD, to senile dementia.

So some real scientists put this claim to the test, and treated just over 3000 elderly people with a high dose of GB. The end result - nothing, nadda, not one damned thing. Those who received the GB under went age-related cognitive decline at the exact same rate as those who didn't get any GB.

And for those of you who want to know what the proven 3 are...

Ginger, for motion sickness
Ginseng polysaccharides (AKA ColdFX) to reduce cold symptoms/infections
Melatonin, for jet lag

And while those work, compared to conventional drug-based interventions, they aren't all that great. ColdFX, for example, reduced cold-virus infections by ~25% and shortens colds by a few days. I actually know a few people who were involved in the developed of this product, and it was developed through hard-core science...and you cannot just use ginseng; you need to eat 5-6lbs/day to get an effective dose of Poly-Furanosyl-Pyranosyl-Saccharide.

Who's dumber?

2009-12-28T12:57:00.006-05:00

So by now everyone's most likely heard of the Christmas-day terrorist attempt. If you haven't the short version is a Nigerian kid became a fundamentalist, built a bomb, smuggled it onto a plane by stitching it into his pants, and then was too stupid to figure out how to make it go boom.

To make matters worse, the security types had been warned about this guy - by his own family. That's right - they (they, as in the TSA and their respective counter-parts in Europe, the UK and Canada) knew he was talking about doing something like this, and didn't do a single thing to prevent it from happening. Even though he was on watch lists, they let him ON THE PLANE.

And the only reason something bad did not go down was our terrorist-wannabe lacked the brain power to figure out how to set off his little fire cracker.

In response to this there has been a new "security" crackdown. The new rulez:

only 1 carry-on bag
no using anything, or getting up to pee, 1 hour before landing
you must be patted down by security before boarding.

The end effect of these new rules - long lines at the airport, cancelled flights, irritated passengers, and the harassment of a guy who had the misfortune of being both of the same nationality as our wanna-be terrorist, and also really having to pee.

Now I fail to see how any of the above, except perhaps #3, could enhance our security while flying. If anything, it seems to be a knee-jerk reaction intended to distract people from the utter failure by those supposedly entrusted with our security. To make matters worse, the news industry seems to have swallowed this hook, line and sinker.

So tell me, who is dumber?

The terrorist, who couldn't blow up his own bomb
The security forces who failed to stop a guy they were warned about well in advance, and who had this guy on their security lists
The news papers, for failing to pick up on #2, and instead are reporting near-solely on the crap done by the morons responsible for point #2 to assure the rest of us that they aren't truly incompetent.

Evolution of the immune system - and making myself a liar

2009-12-23T16:30:00.002-05:00

But a few hours ago I put out a christmas/solstice/new years greeting and said it would be the last post for a while. 5 seconds after posting that my e-mail received a table of contents from Nature Reviews in Immunology which touched upon one of my favourite topics - the evolution of our immune system. I've been out of the immunology loop for a few years, and was pleasantly surprised to see how far that field has advanced.

I've also had a few beers. The combination of ethanol intoxication and my inherent geekyness is going to turn me into a liar - here's another pre-xmas post...

The article requires a subscription. Its so good I'd like to screw copyright and post the whole thing here, but the consiquences of that could be dire, so I wont.

As per usual, a bit of background first.

Since the beginning of life, species have been finding ways to fend off other species that want to prey on them. The classical example is antibiotics - chemicals made by fungi, molds and bacteria, to kill other bacteria, fungi and molds which would compete or prey on them. Not too surprisingly, when life figured out stringing more than one cell together was a good idea, life continued to evolve ways of defending itself against forign invaders.

The first animal systems - innate immunology - was rather simple. Animals simply evolved receptors which identified conserved molecules found on pathogens, but not in the host. Over time this lead to a pretty complex immune system - able to detect viral markers (negative-stranded and double stranded RNA, for example), bacteria (endotoxins, peptidyglycans, CpG DNA) and fungi (cell wall components). But the nature of this system left a - a huge hole - in this kind of immunity.

Simply put, a pathogen simply needed to change these molecules, or find a way to interfere with the detection of these molecules, to avoid the immune system. This was the situation until the rise of vertebrate animals - and is the topic of this fascinating article.

Upon the rise of vertebrate animals - animals with a backbone & centralised nervous system - a huge (r)evolution in immunity occurred: the formation of the adaptive immune system. Without going into a lot of detail, this system generates a series of "randomised" receptors but first combining together 2-3 chunks of DNA (through a process called VDJ recombination). This is further "randomised" through a series of mutagen events. The end effect of this is our bodies make billions of cells, each with a unique receptor. Some of these receptors are non-functional - as in they identify nothing. Others may identify pathogens or other forign antigens. And yet others might recognise out own bodies. Through a process of selection, those which recognise our own bodies are eliminated (errors in this process lead to autoimmune diseases, like multiple sclerosis), leaving behind a set of cells who identify unknown targets.

When a pathogen is encountered any of these cells that identify that pathogen become active, and act to kill the pathogen. But its not just one kinds of cell that does this, but two. B-cells make these random receptors, and when activated secrete these receptors into our blood. You know of these - their called antibodies - and they act to bind up pathogens. A second cell also makes random receptors, called 'T cells", but they don't secrete their receptor. Instead, these cells regulate our immune responses - ramping them up when we need them, and shutting them down (and remembering the pathogen) once sterility has been achieved.

How this system evolved is fairly well established - a virus invaded our genome, incorporated into another receptor, and when things settled down it had created a recombining receptor. Its a fascinating topic, but would be a blog post or five of its own.

What doesn't get mentioned is that this event occurred at a central point in vertebrate evolution - the evolution of jaws. And since this occurred at this point those vertebrates that didn't get the jaws - hagfish and lampreys (see pic on right) also incorporated the virus, developed an adaptive immune system, but did it in a completely different way. In fact, there are some scientists who think it was this differential incorporation of the virus that lead to the formation that lead to jawless verses jawed fishes. And while a fascinating argument, that has little to do with this post. Instead I want to talk about the "alternate" immune system that hagfish and lampreys evolved.

Our immune system is based on the identification mainly of proteins, and often small chunks of those proteins. The "alternate" system is more generic - it tends to recognise larger complexes; often protein-sugar composites. At the receptor level the differences are huge - its blatantly obvious that different genes were invaded by the virus, to make these two systems. But even so, they way these systems work is remarkably similar - the lampreys have two types of adaptive cells, and one of those makes a secreted receptor. The arrangement of the re-combinable genes is simular, as is the mechanism of recombination. And yet the receptors they make are not simular in the least.

This has long been a headache for evolutionary biology - in both cases you have two systems working with each other - a diverse set of elements that gets recombined, and a system to recombine them. But here's when the evolution gets confusing - on one hand we have a conserved method of recombining the genes; suggesting that the recombination mechanism was shared by both jawed and jawless vertebrates. But the target of that recombination mechanism is different - leucine-rich repeats in the case of jawless fish, immunuglobulin domains in the case of antibodies and the t-cell receptor.

The confusion comes from having a case where you've got a conserved mechanism that seems to have evolved inside of two (or three, since antibodies may have done it differently than the t cell receptor) separate processes. While I've talked about the recombination being separate from the target, in reality the two are inseparably mixed - the target of the recombination machinery is an unremovable part of the target pieces.

The end effect of this is that we don't know exactly how the two system separated - at least we didn't back in my day. But today it looks like we now know (see pic at the beginning) - the virus entered the jawless vertebrates, and before any immune system formed the jawed and jawless separated. Then the two diversified - the jawless forming their LRR-mediated immune system, and us jawed vertibrates with our Ig-mediated adaptive immune system producing their immune system.

Last post for a few days

2009-12-23T09:42:00.000-05:00

I suspect that this'll be my last post for a few days, although you never do know...

This atheist is going to spend xmas with his Christian wife and her Christian parents. Sounds awkward - surprisingly, its not. In fact, I'm looking very forward to the time we're going to spend together.

Regardless of your beliefs, I wish you the best in the new year, and a happy solstice-esqe holliday of your choice.

But can I still use the word "pontificate"?

2009-12-21T14:35:00.001-05:00

So the pope has "copyrighted" his name, image and symbols - including terms such as the word Pontiff; his official-ish title. This is only sortof a copyright - its legally unenforceable pretty much anywhere in the world.

None-the-less, it makes one wonder if the terms clearly derived from "pontiff" are still usable, or do they fall under the pontifical "copyright". They're especially concerned about the use of papal terms when people use those terms to imply papal "credibility and authority".

Which brings me around to the term "pontificate" - clearly derived from the term "pontiff", and used in a way as to imply someone is talking in a manner similar to the pope - you know, rambling on aimlessly about topics of which you have no knowledge...

So, can I say "the pope illustrated his usual ignorance when he pontificated about the dangers <sic> of condom use", or does that go against the papal copyright?

T-Cells: Beyond the Resolution Line

2009-12-18T08:44:00.002-05:00

I have a diverse set of research interests - high-end microscopy, immunology, infectious disease, cancer, etc. Its rare that a paper hits the "awesome" end of the scale in most of those categories, but this week Nature Immunology published a paper that got the nerd senses tingling. In this tour-de-force, Mark Davis's group uses a new form of microscopy to analyse how T-cells work.

As usual, a bit of background first.

T-cells are the major regulatory cell of our immune system. The express special receptors, called T cell receptors, which they can use to identify cells which have been infected by bacteria or viruses. After detecting an infection, some T-cells (called CD4 t-cells, or helper t-cells) initiate and regulate the immune response. Another type of T-cell (CD8 T-cells, or cytotoxic T-cells) go out and destroy infected cell.

The t-cell receptors (TCRs) themselves are complex things, with multiple parts (see pic on right). There is the alpha/beta chains that detect the infected cell, and then the CD3 chains and the zeta chains which transmit the signal from the receptor into the cell, and the CD4 (or CD8) co-receptor which helps stabilise the interaction between the TCR and the target cell. Upon engagement these receptors signal by recruiting proteins from within the cell, including one called Linker of Activated T-Cells (LAT), which acts as a scaffold for the rest of the proteins to bind to.

This paper studies the interactions between LAT and the zeta chain portion of the TCR.

The second cool part of the paper is HOW they looked at the TCR. Microscopy is plagued with one major issue - there is a distinct resolution (diffraction) limit, below which we cannot resolve. We've all experienced this ourselves, with our own eyes. Think of driving at night. When you see a car far off you see only one headlight (a, image to the left) - its not until the car comes closer that you can see two (c, image to left). Where the one light becomes two is the resolution limit of your eye; microscopes experience a similar limitation. Under optimal conditions this limit is 200-300nm, while proteins interact in spaces of 30nm or less, meaning we're lacking about 10X the resolution we need to study protein-interactions.

We scientists have a few tricks to get around this limitation. This paper uses one of the newer of these tricks, called PALM. The way this works is you use a photoactivatable dye - basically a florescent marker which needs to be activated by a specific wavelength of light before it becomes fluorescent. The way PALM works is you use a weak activating beam to activate a small portion of the dye. You then image the dye using a high-powered laser, and you image until all of the active dye is photobleached (the microscopy version of burning out light bulb). The resulting image will be a pattern of dots. You repeat this process time-and-time again, and then mix the dot "images" together to get a single, complete image.

Normally this wouldn't produce anything other than what you would get if you just activated all the dye and then imaged it - you'd end up with nothing more than a resolution-limited image. But there's a trick here - known as "math" - which lets us break that resolution limit. Diffraction-limited dots have a specific shape, as you can see in the image above. This shape is always the same, and the "tip" of the peak lies exactly over the fluorescent molecule. So by mapping the peak of each dot, we can "break" the resolution limit and see much finer detail - in the case of this paper, down to 25nm!
So what did they find?

We've known for a while that many of the proteins in our cells membranes are not evenly spread out, but instead float around in little "islands". The clustering of these little "islands" is often what activates these receptors. But in many cases - like the T-cell receptor - we didn't know what was in these little islands, or what happened to them when they clustered. There really were three options:

The TCR and signalling components like LAT are in the same islands, and clustering activates them through mass-action.
The TCR and signalling components like LAT are in separate islands which come together and mix; activating the receptor by mixing normally separate proteins.
The TCR and signalling components like LAT are in separate islands which come together but don't mix; activating the receptor by simply bringing things close together, but without actually mixing.

Davis's group has answered this question. The first image shows the TCR before (left) and after (middle) activation. You can see several small islands on the left, that come together into "super islands" on the right. The right-most image is a control of randomly distributed particles, to show they are looking at islands, not spread-out single molecules.

LAT looks almost the same (image on right), with lots of small islands before activation, and fewer big islands after activation. And while its not obvious when you compare the TCR image with the LAT image, the pre-activation TCR "islands" do not overlap with the pre-activation LAT "islands".

So that answers the first half of our question, LAT and the TCR are in separate islands before activation. But do they mix, or are they wall flowers?
How this was demonstrated is hard to explain; but they used two mathematical measures to figure it out; Ripleys K-function, and cross-correlation, both of which measure how well two distributions overlap. Without going into a lot of boring detail, the TCR and LAT cluster togeather upon activation, but the individual clusters of TCR and LAT remain separate; think of a cookie - both chocolate chips and peanuts are in the cookie, but the chips and nuts remains separate.
So that answers the second half of the question - we've got a couple of wall flowers on our hands.

I'm sure to many this doesn't seem that exciting, but from a biologists point of view this is quite the breakthrough. PALM fast enough to image living cells, while also being able to resolve down small enough to see these little islands. And they resolved something that's been a mystery since those "islands" were discovered nearly 30 years ago - how do they interact, do they mix, and what do they contain. While this is just the tip of the iceberg - hundreds of proteins are known to be in these islands - we finally have to tools to start answering these questions.

Lillemeier, B., Mörtelmaier, M., Forstner, M., Huppa, J., Groves, J., & Davis, M. (2009). TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation Nature Immunology, 11 (1), 90-96 DOI: 10.1038/ni.1832

Atheism - cause or consequence?

2009-12-16T09:04:00.002-05:00

Fellow Torontonian, and far more successful blogger, Larry Moran (of Sandwalk fame) dug up an interesting study just published in Evolutionary Psychology.
To the atheists out there this paper is pretty much old news - nations which are more secular/atheistic are less violent, less crime ridden, and more socially equitable than are more religious nations.

Many take this as proof that religion is evil. While that is a correct position, I wonder if that's really what this paper shows.

Luckily the PDF of this paper is free. Unfortunately, the paper is only available in PDF so I cannot readily post the graphs. So instead I'll provide one example (see image to the right) - in this case we're looking at murder (on the 'Y') verses Religion-Secularism Scale (low = religious, high = secular) on the 'X'. The letters correspond to various nations U = USA, I = Italy, C = Canada, D = Denmark, etc.

Long story made short - this paper quantified the religiousness of a handful of western democracies, and then compared that to a variety of other measures like murder rate, suicide rate, social inequity, poverty rates, STI rates, divorce rates, and so forth. In total religiousness is compared to ~30 different societal measures.
In nearly every case, the more secular societies were better off - lower crime rates, lower degrees of social inequity, longer lasting marriages, and longer & happier lives. Seems cut-and-dried, but a close look at the graphs (including the one above) revealed something interesting - the USA is an outlier in virtually every field. Statistically speaking, this is a bit of a pickle - does this mean the USA is an abnormality that is incomparable to the rest of the countries analysed, or does it mean that the "outlierness" in the religious axis is representative of the "outlierness" of the USA in the other measures?

This is a double-edged sword. If you remove the USA from all the graphs most of the advantages of secularism go away (although some remain - childhood mortality, life expectancy, abortion rate, poverty rate and a few more). But at the same time, removing the USA from the graph also removes most of the "diversity" in terms of religiousness; meaning that we'd be looking for differences over a very small scale.

And, as a final caveat, we have to keep in mind that these are simply correlations - and as every stats teacher out there will tell you, correlation does not equal causation. As such this study doesn't tell us religion = violent, less equitable societies. Its equally possible that violent, less equitable societies = religion.
But my moneys riding on the former, not the latter.

Paul, G.S. (2009) The Chronic Dependence of Popular Religiosity upon Dysfunctional Psychosociological Conditions. Evolutionary Psychology 7: 398-441. [PDF]

Walking the line, using a microscope

2009-12-11T13:37:00.006-05:00

While I oft discuss evolution and autism on my blog, I research neither. My primary interest is actually cell biology, along with a large dose of microscopy. Once in a while a paper will come along which really hits on both of these topics, and its damned well time I blogged about one. So, for once, a posting about a really cool cell-biology/microscopy paper.

It was published just a few months ago (OK, I'm a little behind on this posting) in PLOS Biology: Single molecule imaging reveals differences in microtubule track selection between Kinesin motors.

This paper combines some interesting cell biology along with some cutting-edge microscopy. But before we hit the paper, a bit of background.

Things need to get transported around inside of our cells. For example, proteins meant to detect extracellular signals like hormones must move to the cell surface; otherwise they won't work. Much of this cargo gets moved through small balloon-like structures called vesicles. Rather than drifting randomly, these "balloons" move along tracks in the cell called microtubules; long, filamentous proteins that form a skeleton within the cell. The image to the right shows this cytoskeleton; microtubules are in green (blue is the cells DNA, red is another part of the skeleton called actin).

Like a train, these "balloons" require a motor to pull them along the microtubule tracks. In a cell this job is mediated by motor proteins. While there are a few kinds of motor proteins, this paper deals with one kind called kinesins. Kinesins are proteins which tend to be involved in the movement of proteins from where they are made (ER and golgi) to the plasma membrane. Kinesins are odd proteins, that "walk" along the length of the microtubule in a way that looks kinda like a drunk cowboy stumbling out of a saloon (see the video below).

One outstanding question in the biology of kinesins is how do they know where to go - as you can see in the picture of the cytoskeleton at the beginning of this post, microtubules go everywhere, which makes it hard to understand how things can be selectively moved to specific points in the cell. As it turns out, microtubules are not quite as simple as I outlined here - they're dynamic, as in they continually grow and shrink. But among those ever-changing tracks there are a small number of microtubules that are modified in a way which makes them stable. Furthermore, these stable microtubules do tend to go to specific places - for example, in neurons they lead to the junctions between one neuron and the next. Perhaps these modified microtubules act as highways that allow cells to specifically move proteins to important places.

That is the question asked by this paper.

The real image geekery comes into play with their methods. They used one of my favourite imaging tricks - single particle tracking (SPT) - to follow kinesins while the pull their cargo around the inside of the cell. How SPT works is a blog post or two in itself, but the coles notes version is SPT is a method we can use to monitor the movement of single proteins inside of a cell. Combined with basic microscopy, this method allowed this group to look at the movement of kinesins along microtubules, and to determine which kinds of microtubules these kinesins prefer.

The long and short of how every experiment in this paper was preformed is this group first preformed single particle tracking of the kinesins, overlayed the map of those track with staining of the microtubules, and then used that overlay to determine which microtubules those kinesins are using (click the pic to the right for an example from their paper).

This study looked at three of the kinesins (out of a total of 14), and found that one of them - kinesin 1 - only moves along the modified (stable) microtubules, while two others (kinesins 2&3) moved along all types of microtubules - including those actively growing. Even better, they also tracked the movement of proteins moved by these kinesins, to show that not only the motor, but the cargo the motor carries, follows along the respective type of microtubule.

This paper has confirmed what we long suspected - that some motor proteins follow specific "tracks" in the cell. And while we're a long ways away form understanding exactly how a cell directs this traffic, this paper has provided us our first view of one way that cells direct some products to specific regions of the cell - in this case by using kinesin 1 to move proteins down specific tracks in the cell.

Cai D, McEwen DP, Martens JR, Meyhofer E, & Verhey KJ (2009). Single molecule imaging reveals differences in microtubule track selection between Kinesin motors. PLoS biology, 7 (10) PMID: 19823565

My advice for conferecees

2009-12-11T10:07:00.001-05:00

So it conference season again, and I feel that I should share what little wisdom I have with those who happen to stop by my blog. I originally wrote this to a grad student, so its student-orientated. None-the-less, here's my rules for surviving a scientific meeting.

1) Expect to drink a lot, and plan ahead. Make sure the nights before important days you don't over-indulge. If a day looks particularly boring, chances are it'll be a good day to nurse a hang-over.

2) Look closely at the schedule. Quite often there are sessions which are boring, have nothing to do with you, and represent nothing more then a waste of your time. Those are good sessions to skip, and go do some sight-seeing, shopping, touristy stuff, kayaking, rock climbing, etc.

3) Expect to be constantly tired after the second or third day. Between them, the booze, excessive eating, lack of sleep, and long sessions will kick your ass. Coffee (or other stimulant) is your friend. So is napping through the boring talks.

4) Don't feel obliged to hang out with your supervisor or lab mates. If they're not being fun, attach yourself to another group. Aside from networking (i.e. making friends) this'll also give you the advantage of hearing what people are really doing, rather than the brief (and sometimes misleading) versions you'll get in talks and posters. Of course, if your prof is a party animal, it is your sworn duty to rescue students who have stick-in-the-mud supervisors. Generally speaking, the larger and rowdier the group, the better.

5) You can stay longer if you like, depending on if there is anything you want to do outside of the conference. This is an esecially good idea of you're off-contenent. In the case of New Hampshire, show up late and leave early.  There may be other "New Hampshires" out there - be aware.

6) Some conferences have tours.  Some times they really suck, sometimes they're really 
fun. Best bet - get the details when you arrive and decide from there. You can also often ask the organizers how many students/postdocs are signed up: more = better. If its just profs/spouses, it'll probably blow chunks.

7) Don't be afraid to ask questions. No matter how dumb you may think the question is, chances are that at least half the audience is as confused as you are.

8) Don't be shy about tracking down speakers after their talk, if you want more details. Most are quite open to talking (some are hard to shut up). Plus, you have the advantage of getting them to know your face/name; something that may help when you're looking for your next position.

9) This is the hard part, but let your inner nerd free. Conferences are one of the few places where you can do this, get away with it, and actually end up looking good.

10) Some people use confernces as a place to hook up. If that's your thing, clean up. If not, beware of the romeos sure to emerge from behind the coke-bottle glasses facade.

The Synopsis

2009-12-09T16:52:00.002-05:00

As promised, here is the chapter-by-chapter breakdown of Hovinds "thesis". Hovind claims to have something like 11 chapters in his thesis, but in reality it has only 4 clearly demarked sections. Five if you count the dedication page, and six if you assume his last paragraph is a chapter.

Chapter 1: Introduction

Hovind tells us who he is - he starts by saying 'Hello, my name is Kent Hovind'
Hovind wants to bring us back to the "true faith"
Satan is attacking the world

Chapter 2: History of Evolution

Evolution is a crazy idea
The laws of physics say it can't happen
Evolution is a religion
Small changes are possible, big ones aren't
Evolutions history starts with the fall of satan
In ancient Greece evolution was formed (evolution is all science, btw)
In ancient Greece atheists were formed, and they carried the flame of evolution forward
Most non-Christian religions are atheistic beliefs
During the middle ages there were men who were atheists. They wrote books - evil books. Many were French.
20-some pages in we get to Darwin- or at least his father. His father was an evil, FAT, atheist
Lamarck, Lyell and Darwin were all evil, immoral atheists. They made up evolution because they hate god.

Darwin only gets a 1 paragraph description in this 30-page chapter on the history of evolution!

Marx invented communism. He was evil, atheistic evolutionist

I'd carry on, but you see where this goes. Every individual who may have been an atheist was also immoral, evil and a promoter of evolution.

Chapter 3: The religion of evolution

There is no empirical evidence for evolution
Schools are bad
Religion has not evolved
Taking prayer out of school is bad
Scopes trial was evil
We should either teach evolution and creationism, or neither
Websters dictionary says that religions have divine creators, ergo evolution is a religion
Evolution is the same as humanism, and humanism is a religion therefore evolution is a religion
Humanist manifesto (a book I've never heard of) outlines evolutions desire to take over the world
No missing links have ever been found
Evolution is a religion

Chapter 4: How Old is the Earth

This is an important question
God is not limited by time
What time is it in heaven?
Scientists have hundreds of ways of measuring the age of the earth
The methods scientists use are wrong
The earth is young because of:

comets
helium
the earths spin is slowing down
the moon is receding
science is silly

I think the earth is about 6,000 years old, therefore it is

"Chapter 5" Conclusions
OK, this is one paragraph. It reads:

These honest questions deserve honest answers. I believe we have been lied to about the age of the earth. Satan, the father of all lies, has come up with this to make a fool of Jesus Christ. Jesus said in Matthew 19:4 that the creation of Adam and Eve was the beginning. I believe Jesus was right.

So there you have it, to summarise:

Evolution was created by Satan after the fall
Evolution is a religion
Atheists have carried the flame of evolution throughout the ages
Atheists are fat, immoral, evil, and most likely French. If they're not French, they're fucking someone who is.
The earth isn't old
Jesus said...something
Creationism wins! YAYYYYYYYYYY!

I've read it, so you don't have to

2009-12-09T16:19:00.001-05:00

Todays experiment is filled with long periods where I sit on my ass and waste time - AKA incubation periods. As such I managed to choke down Hovinds thesis in its entirety. To save ya'll hours of painful reading I've prepared a coles-notes version, and if you want to read further, I've added a few comments of my own.

Later this afternoon I should be able to post a chapter-by-chapter synopsis, for those who care. But for now...

Hovinds Argument in a Nut Shell:

Evolution is a new, evil religion (note: religion, not science)
Christianity is an old, not-evil religion and is the sole path to enlightenment

Since evolution is new and evil, while Christianity is old and not-evil, evolution is wrong and creationism is right.

Yep - that's it. I kid you not. 102 pages, and that's what it boils down to.

My comments
This is not a thesis:
I've written a thesis, and I've read several more. And while Hovinds document is many things, it is not a thesis.

Thesis are a pretty standardised document intended to inform readers of new knowledge uncovered by the writer. Almost always they are structured as follows:

Introduction that outlines the area of research, what is known, and what unknown areas the thesis is going to delve into
Several chapters describing the methods used to find the new information, and what the results of those investigations were.
A conclusion which puts the new findings into perspective, and wraps everything up into a nice little package.

Honvids "thesis" does none of the above - his "introduction" tells us that evolution is a religion and evil, he then repeats this same argument over about a dozen chapters, and then he concludes by repeating his introduction. No new info is introduced - and providing new knowledge is the key purpose of a thesis. In fact, most of his arguments can be found in the transcripts of the scopes trial, 83 years ago.

This "thesis" is simply traditional creationist arguments condensed into one article.
I don't think this will be a surprise to many, but the entirety of Hovinds "thesis" is simple repetition of creationist arguments going back decades. Nothing new is added, although Hovind does break up the usual claptrap with piss-poor descriptions of history and character assassinations of various famous (and dead) scientists.

If you've read anything by the "discovery" institute, or any other creationist propaganda machine, you'll have seen everything in Hovinds "thesis" before.

Hovind is frightenly ignorent of basic scientific principals.

In my first post on his thesis I mentioned a few errors Hovind had made in terms of basic scientific principals. Little did I know that was the tip of the iceberg - in one chapter alone Hovind completely fucked up six separate basic scientific principals or definitions. I'm not talking slight errors here - I'm talking 100% wrong; completely polar opposite, of what science truly says.

This is particularity terrifying, as in the beginning of his thesis Hovind proudly announces to us that he has been a high school science teacher since 1976. If that's actually true then he has done irrefutable harm to the education of numerous students over that 30-ish year period. Seriously - the guy doesn't even have a basic grasp of the laws of thermodynamics. How the hell can you teach science when you don't even understand one of the most basic principals science has uncovered?

Just goes to prove how stupid they are

2009-12-09T13:23:00.002-05:00

Kent Hovinds "PhD" thesis has finally been leaked. For many a year he's touted his PhD (you know, that ol' logical fallacy of argument from authority). But while he's touted his PhD, he's steadfastly refused to allow anyone to read it.

Probably because reading it would:
a) cause your head to explode, and
b) make people realize just how stupid he really is

I'm about half-way through - in less than 30min. Pretty sad for a thesis; normally these things are much longer, and not written in the language used by a 5-year old child. The thesis is scanned, so whole-scale quoting is going to be hard. None-the-less, here's a few gems (any spelling errors are mine):

Hello, my name is kent honvid. I am a creation/science evangelist. I live in Pensacola Florida. I have been a high school science teacher since 1976.

As I said, the guy writes like a child.

Where in the world did the idea come from that things left to themselves can improve with time? Who would start a crazy idea like that?

Academics try to be impartial, as to ensure their findings are as rational and objective as possible. Apparently Kent didn't get that memo.

The first law [of thermodynamics] says that matter cannot be created nor destroyed.

Err, no. The first law of thermodynamics states that the energy of a closed system stays constant. You can create/destroy all the matter you want; so long as you obey the E=mc² rule. Oh, and this is his logic behind "there must be a god" - all because the first law says matter cannot be created; ergo, there must be a creator.

Now since the first law allows for matter to be created and destroyed, where does that leave god?

Or, for that matter, if matter cannot be created, what was the creator created from?

The technical definition of evolution is "change".

Wrong - again. The accepted scientific definition of evolution is the change in a populations genetic composition over generations. Lots of evolution (probably most) involves genetic changes that do not result in changes to the organism itself. Its called genetic drift; maybe you've heard of it?

Much of the rest is a confused, obviously wrong in many places "history" of evolution, obviously wrong "history" of modern religion, and various biblical quotations taken out of context to "prove" his case.

A few more gems:

Evolution is purely a religion
Religion has not evolved (and yet he gives a history of its change!)
We go now the the Humanist Manifesto Two written by Paul Kurtz...

BTW, that last one's not a typo on my part; he actually wrote that - double "the", "two" in the wrong place AND the wrong "to".

His thesis is available from wikileaks.

Hat tip to PZ Myers, over at Pharyngula

We may be godless heatherns, but at least our music doesn't suck

2009-12-09T09:32:00.001-05:00

One of my favourite bloggers, the friendly atheist, has come across a real gem of a video. Its a Christian rap group rapping about "side hugs"; cause hugging normally might give you a boner, and that's a sin. Its narrated by another atheist - which is by far the best part of the video.

I feel really sorry for the kids subjugated to this kind of crap. Not only are they having the fairly basic joy of a hug being taken away from them, but they're being brainwashed into thinking that signs of affection are somehow an evil thing.

Not to mention, this music really, really, really sucks!

Compare this to what we atheists have to offer:

and

This seems like a flaw...

2009-12-08T14:49:00.002-05:00

So I am now a follower of my own blog - brining my followers upto 3.

Somehow that seems a flaw; I shouldn't need blogger to update me on my own blog...

Detecting Autism at Birth

2009-12-08T13:28:00.002-05:00

An occasionally-made claim by the anti-vax movement is that autism cannot possibly be genetic because we don't see it at birth. Anyone who has a background in developmental biology is rolling their eyes after reading that, but to many it seems a logical argument.

It isn't, because humans are born with an incompletely developed brain, and as such developmental abnormalities can occur after birth.

But that has little to do with this particular claim, as autism can be diagnosed under laboratory conditions at/near birth. Hence, this claim of the anti-vaxers is yet another of their lies (and boy, do they have a lot of them).

Now one may ask, if autism is detectable at birth, why is it in the real world it isn't detected until 18 months or older? The reason is pretty simple, and I'm going to use two older papers as examples of why this is the case. Both are available for FREE at the links below:

Autism detected AT BIRTH, upto 6mo:
PNAS November 10, 1998 vol. 95 no. 23 13982-13987
Aspergers detected in infancy:
PNAS August 10, 2004 vol. 101 no. 32 11909-11914

In both of these papers autism is detected young - from birth to 6mo in the first paper, and aspergers from 3mo onwards in the second. The later is particularity interesting, as aspergers is a "mild" form of autism often not detected until the age of 5 or older.

If you look at either of those papers you'll see why autism is not often detected in the very young; to detect autism at these early ages requires hours of analysing the movement of these children. On the right I have one such example, of a plotting system used to analyse the movement of arms and legs.

In addition to using rigid analysis of movement, both papers also used pre-set criteria to ensure unbiased measurements. On such example is shown below (on the left) of such a criteria; in particular, the movement pattern of an infant moving from its back to front.

Finally, they looked at facial movements, in particular looking for movements typical of older autistic children.

The conclusion in both papers was clear - the symptoms of autism could be identified in children before six months of age with great reliability.

So why don't clinicians diagnose autism at a younger age?

The answer is simple - the diagnosis of autism at these young ages requires in-depth analysis of hours of video recordings. Even with modern technology, our ability to automate this kind of analysis is very limited. Furthermore, even utilising modern motion-capture methods would require specialised (and very expensive) studios and software. Finally, we'd have to screen each and every child to detect autism, for the simple reason that its unlikely that most parents would recognise the subtle symptoms which occur in infants and seek medical advice.

So contrary to anti-vax claims, autism IS detectable at birth. Unfortunately, a usable and affordable clinical test is a long ways off - in fact, we'll probably have a genetic test long before we have a motion-based one.

Peer review, why do I bother?

2009-12-08T10:25:00.003-05:00

For those of you who know about peer review, you know that the system is broken. But for those of you who aren't in the know, peer review is one of the ways that science journals try to ensure that the studies they publish are properly performed, that the conclusions match the data, and to reduce issues such as fraud.

In theory the process works as follows: You submit your study to a journal, and if it passes the reviewers initial look-over, your study gets sent out to two or three experts in your field who then review your work. They are anonymous (although the authors of the study are not) to protect them from "retribution" if you don't like their review. In theory, the reviewers are supposed to look at the paper, identify any holes, and recommend ways to fix those holes.

Unfortunately, this isn't always what happens. Some reviewers don't put much of an effort into reviewing, so you get half-baked reviews that don't do much to improve the paper but waste a lot of time. Other's will foist off reviews onto untrained grad students or postdocs, and don't vet the review before sending it in. While not always bad, the lack of expertise these individuals have often leads to them concentrating on minutia that is often irrelevant. Other reviewers use the review process as a way to hamper their competitors (whose papers they often receive for review) by recommending unreasonable experiments or even recommending rejection of the paper. And the absolute worst is when you get a real ass hole who thinks you did everything wrong, and demands you rodo every experiment, and rewrite the paper to fit the way they think it should have worked.

To fight this I do my absolute best when reviewing papers, in the vague hope that I may set a good example. I take time to read the paper through - usually several hours, and try to provide reasonable and helpful feedback. In most cases the authors seem to appreciate this and try to address my concerns.

And then there was the last paper I reviewed.

I cannot speak of specifics, due to confidentiality, but the long story short is a group developed a method that is a pretty big advance to one of my fields. Basically, they developed a mass-screening assay for a field that has traditionally used low-throughput methods. As I said, its a big deal - it would have cut my PhD in half, for example. There was one critical problem with their paper though - they didn't actually do the test to confirm that their new readout actually "readsout" what was being measured. To fix that was simple - they had stills from a video already in the paper. All they needed was to do 5min of work and actually analyse that video. I pointed that out, provided a few references in case they didn't know how to do the analysis, and then sent in my review.

In reply, they added the video - without any analysis - to the paper. Or, in other words, they ignored the one recommendation I had, and there is still a gaping hole in their paper.

ARRRRRRRRRRRRRRRRRRRGGGGGGGGGGGGGGGGGGG

So I did the analysis myself - and it turns out their assay works perfectly. It took me a whopping 3min; 2 of which was booting my computer and loading matlab. But this puts me in a real pickle - without that data their paper has a serious flaw, but their method is correct. Normally I'd re-write the editor saying "they need to do this analysis, or reject you need to reject this paper", but since this is a big advance - that works extremely well - I also want to see the paper published ASAP.

Makes me wonder why I bothered putting any effort into the paper. I don't know what I'm going to do yet - but flipping a coin tops the "options list".

Vaccines prevent autism

2009-12-07T11:37:00.002-05:00

I'm sure by now most have heard of the latest anti-science trend, the anti-vaccine movement. For those of you who haven't, an MD by the name of Andrew Wakefield was paid off by a legal firm to manufacture data showing that the MMR vaccine causes autism. His "study" (now known to be 100% fraudulent) led to a war on science, pitting snakeoil salesmen and the parents of autistics they scammed against MDs, scientists, and sane people in general.

The end effect of this has been a resurgence of vaccine-preventable diseases, deaths from diseases which just a decade ago were on the verge of extinction, and all kinds of general mayhem. For fairly obvious reasons, scientists and MDs have been working hard to ensure that vaccines are truly safe, and to tell the public the truth.

Today, another nail in Wakefields coffin has been driven in. A scientific study repeated Wakefields original study, using a larger number of people (192 in stead of 12). In addition, they look not just at the MMR vaccine, but also the measles-only vaccine (as Wakefield claimed it was the measles component that caused autism). Their analysis showed something quite interesting. Instead of seeing what Wakefield saw - an assocaition of autism with MMR vaccination, they saw the opposite - MMR and Measles Vaccines are PROTECTIVE against autism.

In brief, the MMR vax reduced the chance of getting autism dramatically (odds ratio of 0.17, 95% CI: 0.06-0.52) and the measles vax reduced the chance of getting autism but not quite as much (odds ratio of 0.44, 95% CI: 0.22-0.91).

I'm sure the anti-vax loons will promptly be telling us this is all part of some conspiracy, but non-the-less, the fact the got such a striking finding using Wakefields own methods pretty much confirms what we all know - Wakefield lied about his results.

One less reason...

2009-12-07T11:01:00.004-05:00

I've long been a critic of the whole "organic food" thing. As someone who grew up on farms the whole thing seemed like BS - its well established that the green revolution lead to greater amount of healthy food - how going back to the pre-revolution days could improve that was never clear to me. Over time science has shown my suspicions to be correct - organic food is neither healthier or more environmentally friendly.

Basically, "organic food" is a way of scamming money out of stupid people.

But I have long been a fan of buying locally-produced food. The benefits of this were supposed to be two fold - you help local farms (thus reducing the expansion of so-called "industrial farming") and you were helping the environment by not buying food that had been shipped from half way across the globe.

The first half of that equation is still true - buying local supports local farmers, and helps to keep family farms in business. I have to admit a strong bias here - most of my family remain farmers, and I'd like for them to keep their livelihood.

Unfortunately, the second half of that equation is no longer true (at least not in all cases). In hindsight this was an obvious thing, but rose coloured glasses do tint one's view of the world.

It turns out that it is often more efficient to ship foods from afar than locally, for a few reasons:

The assumption that closer food production = lower transportation emissions ignores everything leading upto that local production - shipping of fertilisers, seed, etc. Thus, the footprint of a locally produced food may be the same, or greater, that distantly produced food simply because there isn't a fertiliser company, or seed production firm, near buy.
The assumption that closer food production = lower transportation emissions also ignores the efficiency of transport - as much as we like to ignore it, the fact remains that cargo ships and trains have much lower emissions per tonne transported than does a truck or car. In other words, shipping food across a continent to a central distribution centre; and from there to stores, may be more efficient than having hundreds of small trucks transporting local produce to those same markets.
Bulk production is often more efficient than small-scale. In plain English, that simply means that a large mega-farm can often produce the same amount of food for less emissions than a smaller farm.

Obviously the equation is a lot more complex than many assume, and whether or not local food is more environmentally friendly is going to vary crop-to-crop and region-to-region. According to the news last night the analysis has now been done for one food - farmed salmon - and the news ins't good for local producers. Turns out, shipping salmon from mega-farms in Asia produces less CO2 than importing equivalent amounts from the smaller farms which are common here in North America. I'm still trying to find the actual paper, but if the news report was correct things do not look good for using local farming as a way to reduce transportation-sourced CO2 .

The genetics of autism and schitzophrenia

2009-12-04T08:39:00.003-05:00

Wow, 1.142857143 week & two posts - something must be wrong with me.

Anyone who knows anything, knows that autism is largely - if not entierly - a genetic "disorder". Disorder is in quotes since I think its arguable that some forms of autism represent normal neurovariation, rather than a disease/disorder.

Anyhoo, its also been long known that schizophrenia is also a genetic disorder, and as we've delved into the genetics of both diseases we've found some startling things - notably that many of the genes linked to one disease are also linked to another.

In the early edition of PNAS today (or at least I noticed it today) is a paper that looks at these linkages closely, and finds something very interesting. But before we go into that, lets set the stage:

One of the more common, but least understood, forms of human genetic variation is copy number variations. This simply means that some people will have more copies of a particular gene that others, and some will have less. This can result in biological abnormalities, as some genes need to be present in the right "dose" - too little or too much equals trouble. Many of the genetic variations found in autistics and schizophrenics are these kinds of variations - extra copies, or missing copies of genes.

In this particular paper, Crespi, Stead & Elliot show that autism is schizophrenia's genetic opposite - in cases where schizophrenics have gene duplications, autistics have gene deletions. And the opposite is also true - where autistics have duplications, schizophrenics have deletions.

This is a very interesting finding, as it tells us a lot about what is going in these disoriders. Notably, autism seems to occur when genetic mutations remove the breaks of developmental pathways - autistics seem to have unregulated brain development. Schitzophrenics seem to be the opposite - rather than having out-of-control brain development pathways, they instead have broken brain development pathways.

Of course, the anti-vax loons will ignore this study, and all that in means, inorder to preserve their faith in the non-truth that vaccines cause autism.

Why is it they're always so nice to you after ripping out your heart?

2009-11-26T15:15:00.004-05:00

So its been a long while since I last posted something. In my defence I did just get married...don't worry that has no relevance to the title. It's just my excuse (and what a good one it is!) for not posting is so very long.

As for the title - and perhaps explaining a little more of my absence - I just finished a magnificent study. At least that's what I thought, why my colleagues thought, and what the audience thought at the various conferences where I presented the work. The editors of Science, however, were not so enthusiastic - they rejected the paper.

Not the getting rejected from Science is such a bad thing. Its only one of the most prestigious science journals in the world, and they are known for rejecting something like 95% of the papers submitted to them.

So I wasn't mad about getting rejected, but the editors comments drove me nuts. What they write is: "your work is fantastic", "we really enjoyed your paper", etc, etc, etc. And after getting you all buttered up and felling all warm and fuzzy inside, they drop the bomb and reject the paper. Why they don't just come out and tell you the truth, I'll never know. I'd rather get "your paper sucked for reasons X, Y and Z, so please fuck off and done write back". Instead I get "our decision is not a reflection of the quality of your research but rather of our space limitations".

ARRRRRRRRRRRRRRRRRRRG

While this video addresses reviewers, not editors, it's pretty much a play-by-play of my response this morning. The only differences: I have less hair, I speak English, and there was a little more profanity in my version...

Another blow against the anti-vaccinationists

2009-05-28T09:38:00.002-04:00

As many people know there is a lobby of sorts out there - their goal is to get people to replace vaccines with "naturalpathic" non-cures for disease. This is the Jenny "Indigo Child" McCarthy's line of crap. Their line is simple - vaccines cause autism. Which, of course, is absolute BS. But the millions they make selling their books, TV appearances and woo "cures" outweighs truth - at least in their minds.

Today, science (both the study of, and the journal) made not one, but two more blows against this non-sense. These blows came in the form of two separate studies looking at the genetics of autism.

In the first study, by Hakon Hakonarson group in Philadelphia found a strong genetic linkage - meaning they found genes that were inherited preferentially in autistics - on chromosome 5. These genes, called cadherins, help neuronal cells stick together. Mess with these proteins and neurons are going to have trouble making connections. Poor connections = autism.

In the second study, also from the Hakonarson group, a screen of the whole human genome identified a second set of genes, which regulate ubiquitin ation, as also being linked to autism. Ubiquitination is used by our cells to target proteins for destruction. The failure of proteins to be destroyed is a cause of several neurological disorders, the classic example being Alzheimers. To my knowledge, this is the first indication that there may be a failure in protein degradation in autistics. But if this finding holds true it would go a long ways to helping us understand - and perhapos treat - autism.

Hey Jenny - its the genes, stupid.

I doubt she'll get the memo...

Our science minister is an IDiot

2009-03-17T11:00:00.004-04:00

Wow, one day two posts - who knew there would be so much in the news to piss me off today!

So apparently my countries science minister is a creationist, or at least dumb enough to think that evolution has something to do with religion.

“I'm not going to answer that question. I am a Christian, and I don't think anybody asking a question about my religion is appropriate,” Gary Goodyear, the federal Minister of State for Science and Technology, said in an interview with The Globe and Mail.

From The Globe and Mail.

Of course, this is the same douchebag who cut science funding in our country by over 100 million, yelled at scientists who had the gall to point out the negative effect this would have on Canada's long-term scientific progress and industrial growth, and who is a chiropractor pretending to be a doctor (yes, he calls himself a doctor).

Maybe someone should point out that evolution is a scientific theory and has nothing to do with religion. Or, that many Christians see no conflict between their beliefs and evolution - say the clergy project for example.

Of course, we could point out that there is no god, and his religious beliefs are fraudulent. But hey, for that to work Minister Goodyear would have to be a rational - and lets face it; we're dealing with someone who thinks that bending peoples spines makes him a doctor...

The pope speaks - people die.

2009-03-17T09:13:00.002-04:00

So today the pope opened his fat mouth, and repeated the usual Catholic line of "condoms are evil, the only way to fight HIV is abstinence" line of bullshit.

Gotta love it - a 70 year old virgin who wears pajamas to work, telling us how to control a sexually-transmittable disease.

And, of course, his claim that abstinence is all thats needed to stop the HIV epidemic is pure, unadulterated bull shit. Even if we stopped all sexual transmission of HIV, its still transmitted by IV drug use, contaminated medical equipment, during childbirth, via breast feeding, and via contact with blood and other bodily fluids of an infected individual.

History has taught us waht doesn't work - abstinence-only programs top that list. One needs to look no further than the USA's experiments with these programs - increased rates of STD transmission, increased rates of teen pregnancy, kids with syphilis, and whatnot. Likewise, abstinence-only HIV prevention has also failed - and failed big time.

What actually prevents HIV transmission is broad-based programs orientated towards risk reduction. These programs include a mix of abstinence, condom-use, safe drug use, and frequent testing. Yes, abstinence is a part of the program - but not the whole thing.

I secretly hope the pope will one day pull his head out of his ass, and join us in the real world. But then I remember that he is the head of a church who hid child-rapists and welcomes holocaust deniers.

Of course, they did apologist for persecuting Galileo - 358 years after he died. So, if you're still kicking on May 17th 2367, tune in your holotv for the space-popes apology to the millions the Catholic church killed due to their asinine policy on condoms.

Until then, please don't listen to him.

ID my ass - AKA Life is just weird.

2009-02-24T14:14:00.008-05:00

Deep see marine life is among the most unusual and bizarre life on our planet. Fish whose jaws are bigger than their bodies, fish with double-jointed jaws who can swallow prey larger than themselves, even fish with glow-in-the-dark fishing rods...

...PZ Meyers, of Pharyngula fame has pointed out one of the weirdest ones yet - it has a transparent head, and its eyes are INSIDE the skull! Check out Macropinna microstoma.

Those eye-like things above the mouth are its nostrils. Its eyes are those green blobs INSIDE ITS SKULL!

Lots of more pics of this dude can be found at MBARI.

Now, creationists and IDists will tell us this beastie was designed. I ask - what god would design this? A drunk one, a stupid one, or one who's just plain board?

And just to add something new - The video:

Andrew Wakefield - Worst Man Alive

2009-02-11T12:08:00.003-05:00

This has been making the rounds around the blogs, but its worth mentioning again - and again - and again.

Some of you may be familiar with Andrew Wakefield; the British MD who, in the late 1990's, reported an apparent link between vaccination and autism. The study was small - only 12 people, and the results purely correlative, but it set off a firestorm which lead in many nations to a decrease in the vaccination rate.

Scientifically, the Wakefield study was always suspect - correlations prove nothing, and dozens of other studies using larger groups of people could never find a link.

Turns out that because the Wakefields study was a complete and total fraud. None of his patients had the GI problems he claimed, and several were identified has having a neurological disorder long before they were vaccinated.

This talking head pretty much sums things up - the good part is near the end.

Visit msnbc.com for Breaking News, World News, and News about the Economy

Marmite vs. LB

2009-01-27T14:58:00.005-05:00

Sometimes my knowledge of science is a bad thing - like when I read the ingredients list of a chocolate bar (not that it stops me from eating it, but really, does hydrolyzed soy protein & soy lecithin really need to be in there?

The flip side is that it does ensure that I never eat some things - like Marmite.

For those of you unfamiliar with marmite, its a filthy concoction, invented by the English (who else). For those of you who have not had it, it tastes something like what you'd get if you washed week-old socks in lye, and boiled it down into a thick paste. Pretty nasty stuff.

Its made from dead yeast, basically a way of using the byproducts of beer manufacture to make something healthy (its full of vitamins), but without any other redeeming characteristics (and quite a few not-so-redeeming characteristics).

Back to how science tells me this stuff should not be consumed by humans...

Marmite shares remarkable similarity - one may even say "its pretty much the same shit" as LB broth. Those "in the know" already know the virtues (or lack thereof) of LB, but for the rest of the world LB is what scientists use to grow many types of bacteria - usually E. coli. When you walk into a lab and smell an acrid smell that is a combination of month-old beer, gym socks and something that cannot be described - that's LB. It has the appearance of urine, its sticky if you're unfortunate enough to spill it, and its the cats meow as far as bacteria are concerned.

More to the point its made from the same thing as Marmite - dead yeast. Basically its dilute marmite. The bacteria we usually grow in it come from poo. That's right, marmite is indistinguishable from poo, as far as bacteria are concerned. I wouldn't eat poo.

Would you?

Where I've been

2009-01-14T11:48:00.003-05:00

A few maps of the USA/world have been making the rounds on some of my favourite blogs. Here's mine:

visited 22 states (44%)
Create your own visited map of The United States or try another Douwe Osinga project

Can you tell that I tend to drive, not fly, from Canada to the US?

visited 8 states (3.55%)
Create your own visited map of The World or try another Douwe Osinga project

My world tranvels are not quite as extensive as I would have hoped...

Diagnosing Psueodscience

2009-01-08T12:13:00.009-05:00

So apparently at least one person reads my blog! That means my audience is infinitely larger than I previously thought.

In my last post, William Nedblake, author of one of my favourite blogs (Skiing Mount Improbable) gave me a little encouragement to continue blogging in the new year. Never to be one to disappoint my fan(s), here it is.

Actually, I should be honest, this is something I prepared years ago for a series of talks on science in the public I was invited to attend. Unfortunately, I never gave the talk, so instead I've converted my notes into full paragraphs, and blog-ified it, which in an odd way that makes this fresh material...

-----------------------------------------------------------------------------

This post is about pseudoscience, and how to identify it. Today, the internet and media is so full of pseudoscientific babble that it is becoming harder and harder to separate real science from pseuoscientific nonsence. I hope to clear the air a little in this post, by showing the difference between valid science and pseudoscientific nonsence.

Firstly, what is science. Simply put, science is a method of understanding the physical universe based on observation and experimentation. Scientific concepts can easily be identified through the use of things like data, statistics, hypotheses and formal theories. Most importantly, the claims of science change as new data and observations become available, and scientific theories are based on all available data – not just the data that is convenient.

Pseudoscience is quite different – pseudoscience is bull shit mascaraing in the guise of science. Pseudoscience often uses scientific terminology, credentials, and even little pieces of real science to support their claims. However, where they differ is that they are based on concepts not supported by evidence, and often pseudoscience exists in opposition to how science has shown the universe to function.

Examples of psudoscience abound – creationism & intelligent design, homeopathy, alternative medicine, naturalpathy, HIV-denialism, the anti-vaccine movement, and scientology are just a few examples of the pseudoscientific movements out there.

So how do you tell science from pseudoscience – its easy, here's my 13 point list of how to identify pseudoscience:

1) Attacks on mainstream science. This is the cornerstone of all pseudosciences; since pseudoscience is based on myth, they cannot counter real science with facts and observations. So instead they resort to attacks on scientific concepts, scientists, and any other individual who doesn't buy into what they're selling. There are simply too many examples of this to begin listing them -one need look no father than the comments posted on more popular blogs like Pharyngula, Sandwalk or Skiing Mount Improbable.

2) Tunnel Vision. Pseudoscience often takes a very simplistic view of the universe, and attempts to interpret all facts to fit that view. This usually inv
olves intense analysis of facts that support their position, while ignoring facts that counter their position. Take the creationists claim that the second law of thermodynamics prevents evolution. They concentrate on the part that says “entropy must always increase”, but ignore the “closed system” bit. Unfortunately for them the earth is an open system – new energy is continually provided by the sun, and entropy is constantly reduced through the emission of infra-red radiation.

3) Distortions of scientific theories. Often, pseudoscientists will misrepresent the claims of a real scientific theory, in order to discredit the theory. Creationists are notorious for this, by often creating their own versions of evolutionary theory that are so bizarre and unrelated to the real theory of evolution as to be meaningless.

4) Refusal to examine contradictory evidence. Denial isn't just a river in Africa, its also the key method that pseudoscientists use to maintain their beliefs in an universe that runs contrary to the way they think it does. You can point out as many facts and papers as you want, they just ignore it.

5) Exaggerated complexity. Sc
ience is a reductionist approach – meaning it breaks complex problems down into small parts, and then figures out the way each of those little parts work. Once we understand the small bits, we can then understand the whole. Pseudoscientists often use the opposite route – they have claims and ideas so complex as to make them completely unintelligible. After all, if an idea is so complicated that they cannot even describe it, how could anyone ever disprove it? Usually this tactic is nothing more than an attempt to make it seem like they know a lot more than they do. Don't forget, renowned theoretical physicists like Richard Feynman and Stephen Hawking can distil their extremely complex theories into plain English, and if they can do it than any real science can also be explained in laymans terms.

6) Mass use of scientific terminology. Psueodoscientists like to use jargon. Lots of large, complicated words designed to make them sound smart. They often use the terms incorrectly, which is the key to identifying this tactic.

7) Unverifiable sources. The key element in scientific discussions is the ability to show where your information is coming from. This usually occurs in the form of citing a source – often an article in a scientific journal. Since pseudoscientists don't have facts, they don't have reputable sources to cite. So instead you get sources that no one can access. Another variant of this is citing a source that simply makes the same claims. Apparently, pseudoscientists think repeating the same claim again and again counts as evidence.

8) The use of logical fallacies. There are dozens of these – it would take several hundred pages of text to describe them all – so instead I've included a link the wikipedia article on logical fallacies. One example of a logical fallacy is an appeal to authority.
This is when a pseudoscientist says something like “Dr. Behe, a biochemist, says evolution is wrong, therefore evolution is wrong”. Simply because a supposed expert thinks an idea is BS doesn't make it so. Another common logical fallacy is an argument from ignorance. This simply goes “that idea doesn't make sense, so it must be wrong”. Being too stupid to understand an idea doesn't mean the idea is wrong – it means you're stupid.

9) False or irrelevant credentials. Many pseudoscientists will claim to have credentials that they don't actually have – naturalpaths and chiropractors who call themselves doctors, despite never having gone to medical school being a common example. In other cases someone with an irrelevant credential will try to use it to give their argument weight. There is one famous economist who claims global warming is a hoax, and uses his PhD to lend weight to his arguments. Thing is, he never mentions its a PhD in economics, not in climatology.

10) Fraud, lies and distortions. Pseudoscientists lie a lot. Sometimes they simply distort real scientific findings, but more often than not they just making things up. A prime example of this is the HIV-denialist movement. One of their most common claims is that HIV has never been isolated. Thing is, 2 seconds on google will bring up pictures of purified HIV (right), protocols for preforming such isolations yourself, and for that matter, companies that will sell you kits to purify HIV in three easy steps.

11) Leaps of faith. This is classic pseudoscience at its best. State a real fact, claim it leads to a certain interpretation or hypothesis, and then claim that interpretation or hypothesis to be correct. Young-earth creationism is ripe with this stuff – carbon 14 dating is inaccurate past 60,000 years, so the earth can only be 10,000 years old. The first part is correct, but how the hell they come to the second conclusion is a mystery.

12) Publication mills. To keep up with their growing attempts to appear legit, some pseudoscientific movements like the intelligent design movement have gone to the extent of creating their own pseudoscience journals. They then publish papers supportive of their position in those journals. Luckily, these are easy to identify. If an scientific journal isn't listed in databases like google scholar, pubmed, or the Web of Science, its probably not a real science journal.

So there you have it twelve easy ways to identify pseudoscienctific nonsence. Oh wait, I promised you 13. The last ones an easy one – if it sounds too good to be true, its probably pseudosciene.

PS: Sorry about the crap formatting; for some reason blogger keeps screwing it up.

Should post something

2009-01-07T14:41:00.002-05:00

So apparently I'm not a good blogger - almost two months without a peep. My excuse - I don't have one. I'd make a resolution to write more often, but that would guarantee I wouldn't (haven't kept one yet, why start now).

Happy new year.

Science through EBay

2008-11-20T10:26:00.003-05:00

The wolly mammoth genome was released today in the prestigious scientific journal Nature. And while this represents an amazing and wonderful success, I'm not going to mention the contents of the paper.

Instead I'm going to comment on what the researchers said while being interviewed on the science podcast.

Apparently they bought the mammoth hair that they used to isolate the DNA from EBay!!! Now scientists have long used ebay as a source for used scientific equipment - I myself bought a microscope and a few objectives through ebay (and got a steal of a deal on it too). But this ahs to be the first time I've heard of anyone buying a reagent from ebay; nevermind a piece of a mammoth.

In fact, I'm 99% sure you're not supposed to sell biological materials via ebay.

Its science wierdness at its best. If you're interested in the interview, you can use the player below to listen to it. The mammoth interview runs from 1:25 to 10:51; the ebay bit is at 2:10-2:3:20.

Love it!

Ignorence wins, freedom and equality looses

2008-11-05T10:33:00.005-05:00

So like every one else in the world, I'm going to blog on the results of the US election.

But I'm not saying a thing about Obama, McCain, or the senate.

Instead I'm going to write about the death of equality in the US. Tragically, proposition 8 passed in California; meaning it is once again illegal for homosexuals to be wedded in the Garden State.

Many have claimed that this will have no effect; they can still have civil unions. You'd think after the 1960's civil rights movement this kind of crap wouldn't stand. After all, it used to be "equal" to have separate water fountains for blacks and whites. It used to be "equal" to have bus seats for blacks and whites. It used to be OK to be "separate but equal".

Everyone today knows that's all bullshit, that "separate but equal" actually means "discrimination with a smile".

And yet, once again, "separate but equal" has reared its ugly head. And this time its affecting one of the largest legal statuses an individual has. With marriage comes power of attorney over an incapacitated spouse, joint property rights, tax benefits, inheritance rights, and a whole whack of other legal rights and responsibilities.

Last night, those rights and responsibilities were arbitrarily stripped from numerous couples, all because some people decided that bronze-age mythology should rule over the concepts of equal treatment for all that the USA was supposedly built upon.

Most tragically, this morning numerous loving couples who have committed to live their lives together awoke to find their marriages nullified - without their consent, and without recourse.

Congratulations California - you've taken one huge step back towards the dark ages.

Image from Liberty Unbound.

Been gone a while

2008-10-15T18:04:00.002-04:00

So I realize that I have not written anything in a while. In my defence, over the past two weeks I have:

Moved (I hate moving, but it had to be done)
Was sick - very, very sick
Voted in a new Canadian government
Spent all my money (on moving)

About all I have to say about all the above is - thank goodness we got another minority government. As you may notice in my previous posts, I hate all the parties. By having a minority the gov cannot get a lot done, and therefore cannot screw up our lives too much.

Its the best bet we have

I voted for the conservatives - ys I hate them, but they were guaranteed not to win in my riding. My riding went to the liberals, but by one less vote...call it registering my dislike of the political system.

Hopefully I'll have some real content soon...

Charity, atheist style

2008-09-30T13:12:00.003-04:00

So I've volunteered and donated to charity for most of my life (my charity was lacking in my earlier years, but what do you expect - I was still in diapers). I've generally leaned towards volunteering, but due to the time constraints that come with growing up, I've begun to "express" more of my charitable efforts through donations.

This has led to a "moral quandary" of sorts - many charities are religiously based, and as an atheist I am uncomfortable donating to such non-secular organizations. The reasons are simple, as listed below:

Many such organizations use their charity work as an opportunity for missionary activities. Obviously I do not support the spread of religion.
Even if an organization isn't openly missionary in their work, the pressure is still there as people making use of the charity will be interacting with people who share the same religious leanings as the charity itself.
Access. Some countries limit the access of religious groups, meaning that faith-based charities have less ability to reach those in oppressive regimes - who often are the most in need.
Trust. Past experiences with some Christian charities bordered on the edge of fraud. So I don't trust them much anymore.

Much to my happiness, there is Kiva, an organization which collects funds and distributes them to micro-loan organizations. Because I can select my projects, I can ensure my money goes directly to people who need it most, and I can avoid non-secular organizations.

Are you an atheist? If so, join the Atheists, Agnostics, Skeptics, Freethinkers, Secular Humanists and the Non-Religious team on kiva. A great community of non-secular individuals working to make the world a better place, one small loan at a time.

Almost election day

2008-09-30T09:46:00.002-04:00

So its almost election day here in Canada (well, for me anyways; I'm voting on the early poll). And despite being a few days away from voting I'm still undecided. Long story short, I hate all of the parties, and cannot find anyone who I could vote for without having to void my bowels first. The breakdown of my choice:

The liberals: The most divisive party in our country, and its only through blind luck that these idiots haven't destroyed our country yet. When in power they had a reputation (deserved, BTW) for illegally "punishing" one or two provinces to make themselves look tough on whatever was the hot political topic of the day. Basically, sacrifice the rest of the country to get the vote in Ontario and Quebec. And they want to put us back into deficit funding...

The conservatives: my fallen hero's. Back in the day we had the progressive conservatives - hands-off the economy, pro-social services, pro-trade. We generally did well under them, and they balanced out nicely with the libs. But they're dead and gone, and in their place is the new conservatives - overly religious, highly right-wing, anti-social services, anti-poor, anti-environment, anti-everything that is good about our society. Bush likes them; reason enough not to vote for them.

The NDP: basically communists in disguise. Pro-union, anti-economy, anti-common sence. Probably the greatest threat to the Canadian economy out there.

The green party: Pro-environment, and don't have a logical thought on any other topic. Last election they got my vote - not because they earned it, but because I was voting in the hope of having more options next election. They won't be getting my vote this year, a one-issue party has no place in national politics.

The bloc: Quebec-only party (so I can't vote for them). Want to destroy Canada; if there was any justice in the world they'd all be strung up until their heels stopped twitching.

So who do I vote for - I don't know. Does the marijuana party run anymore?

We're the oldest!

2008-09-26T09:53:00.003-04:00

Great news from Canada's frozen north - the oldest rocks on earth have been found; they formed just 300 million years after the earth collesced out of the protoplanetary disk (AKA 4.28 billion years ago).

Viva la Canada!

Creationists take note: to get this to fit to your delusion, divide those numbers by 450,000. Which makes these rocks about 9,511 years, 40 days, 13 hours and 20 minutes old.

Post-doc glut, or training behind the times

2008-09-25T09:40:00.003-04:00

Earlier this week the leading journal science featured an article on the lack of tenure-track positrons for new researchers.

Long story short - this article tracked the placement of several post-doctoral fellows who "graduated" from a prestigious program at Yale in 1991. Of the 30 post-docs that were tracked, only one ended up in a tenure-track position.

The main point of the article was that there isn't enough positions for post-doc. I think they missed the mark - big time.

Long gone are the days where the major end-point of a higher education was academic research. Over the past few decades many other options have become available for PhD and post-doc level trainees. Many people - myself included - enter their PhD's expecting to enter one of these other routes.

Many non-tenure academic research positions exist - especially in research institutes and hospitals. Outside of the academic world there is government and military research, biotech/pharmaceutical companies, teaching, "think-tank" and public policy organizations, numerous non-research government jobs, investment advisers, and many more - and all of whom expect PhD or post-doctoral training.

If anything, the nature article reflects not a problem with the tenure-track job market, but rather represents the degree to which academic training and expectations are living decades in the past.

The problem isn't that most of these postdocs didn't get tenure-track positions.

The problem is that current training programs do not reflect the modern biological research/industry world or the expectations of current trainees.

Tenure-track positions have long since faded as the major reason people enter higher education. Maybe its time the training begins to reflect that.

Not dead, just busy

2008-09-24T13:09:00.004-04:00

So I'm 99.9994% sure I don't have any regular readers, but regardless I feel that I owe an explanation over why there haven't been any updates for a while. You see, I am busy, and before I was busy I was using the blog to fill in my boredom. Yes, there was a brief time when I thought I'd be the next PZ Meyers, or whomever, but that moment has passed - hell, I don't know where he finds the time to write as much as he does.

Anyhow, I should get around to writing something real, hopefully soon. But between work, moving and planning a wedding I'm not exactly flush with free time...

Good idea, or bad idea

2008-09-18T08:41:00.002-04:00

An interesting news article appears in todays edition of Nature. Its about a group of scientists who are sharing their data as it is generated, instead of going the normal route of keeping it secret until a conference or publication.

This is an interesting idea - it would eliminate getting scooped, as there would be a public record of who truly made a discovery first. Likewise, it could make for better science, as people would be able to look at your results (before or after a publication) to see if there are small details that didn't get described - details that may lead to something interesting. Likewise, it would be a big inhibitor of academic misconduct, as reporting findings as they occur would limit fraud, and make it easy to check that papers results match the original data. That said, I see some major drawbacks; and unfortunately, the article concentrates mostly on patent issues, which in my opinion misses some of the major points.

I think I covered most of the positives above, but some big problems that need to be ironed out:

Data mining. Experiments represent a huge investment - in time, money and "intellectual capital" (i.e. you tend to spend a lot of time planning and thinking before you even do the damned thing). By posting results as they happen, others could parasitize off of you, and mine your results for information that they then publish - and get credit for. People could have successful scientific careers without once entering a lab, or having ideas of their own.
Practicality. As I mentioned in a previous post, I can generate several gigabytes of data a day. How do I share that? Who pays for the data transfer costs if people download gigs of data over our Internet connection?
Fraud. To prevent others from mining their data, or to mislead their competitors, some scientists (not me!!!!) may publish false results. And if such false results are found, what can be done about it? How do you differentiate between a false result and an accidental error?
Credit. How do you give credit if you see some of this data, and it gives you an idea that allows your own scientific program to advance? Normally we would cite the relevant paper where we got the idea from; how to you cite a lab book?
Accuracy. Before being published, scientific articles undergo peer review. This process ensures accuracy; that conclusions match data, that experiments were preformed properly, etc. Publishing a lab book would bypass that step, and erroneous results or methods could be as misleading; potentially even more misleading as deliberate fraud.
Archiving. If this practise became common, and people began citing lab books directly in the scientific literature, then we would have to permanently archive this data so that future researchers could look back at it. Who will be responsible for that - The journals? The research institutes? The researcher themselves? Who will pay for it? How will it be formatted? Stored on-line? Available to all? Available upon request? Removed to off-line storage after a while? If so, how long do you keep in on-line before moving it off-line? Etc, etc, etc.

So a cool idea, one which could help advance science and reduce fraud. But an idea which has serious issues that need to be worked out first.

Basic science question, neat paper

2008-09-17T09:49:00.003-04:00

Most of us scientists spend a lot of time reading (and writing) papers about biological minutia; the fine details of isolated biological processes. And while this work is important, its nice every once in a while to read a "big picture" type of article.

This week, in the Journal of Cell Biology, a interesting paper on how the nuclear envelope reforms after cell division was published. This paper is one of those big-picture papers, and something that I found to be really cool.

To make a long story short, each and every one of our cells (except platelets and red blood cells, but I digress) has DNA. This DNA is stored inside of a membrane-wrapped region called the nucleus. The membrane surrounding the nucleus is called the nuclear envelope, and its job is to keep things that are supposed to keep the right things in the nucleus and keep the wrong things out.

Problem is, when a cell divides it needs to make sure each of the daughter cells gets a copy of the DNA, but that DNA is hidden away behind the nuclear envelope. We know that the nuclear envelope is connected to another sub-compartment in our cells called the endoplasmic reticulum (ER), and during cell division the nuclear envelope gets absorbed into the ER. What we don't know is how the nuclear envelope reforms, and that is what the paper is about.

What Anderson and Hetzer showed was that the new nuclear envelope formed through a rather simple process, which is driven by a small family of proteins which control ER shape. These proteins, called reticulins, give the ER shape by curving the ER membranes into small tubes. During the reformation of the nuclear envelope, extensions of the ER bound to the telomeres (ends ) of the chromosomes. Next, membrane gets pulled out of the reticulin-formed ER tubes, making a sheet that eventually covers the DNA and makes the nuclear envelope. Finally, nuclear envelope proteins (which don't like being in curved membranes) migrate to the flatter nuclear envelop; vola - nuclear envelope.

Cool study, although I have to admit, I find it a little shocking that such basic biological questions are still being worked out. You'd think we'd have a handle on all the "big picture" stuff by now...

About the pictures: the top image shows the ER (green) binding to the DNA (red), from the Journal of Cell Biology. The lower image shows chromosomes (blue) being pulled apart by microtubules (green) during a cell division, image is from wikipedia.

Saturday musing about blogs and evolution

2008-09-13T13:22:00.003-04:00

This week in science there was a fascinating article on the rise of dinosaurs and the fall of crurotarsans (crocodile-like animals that were the chief competitors of dinosaurs upto the triassic extinction event).

The take some message of this article was that the survival of dinosaurs appears to be a random event. There is no evidence that the dino's were better evolved, more diverged, or evolving faster when the triassic extinction event occurred. Instead, plain dumb luck seemed to be the factor of the day.

I for one was not too surprised by this. Much of evolution is dumb luck - the effects of mutation are random (even though their localization in the genome is not; some areas mutate much faster than others). Likewise genetic drift - the random changes in gene frequencies - is also a major factor. The idea that a random environmental change could produce an apparently random pattern of extinction should not come as a surprise.

That said, I'm wondering if there is a missing factor here, something that may make this random event a little less random. The problem that I see is that the paper purely analyzes the pre-Jurassic species, and does not look at the dino's who survived the Triassic-Jurassic extinction event (TJEE). In plain terms, they showed that there was no difference between dinosaurs and crurotarsans as groups that would explain the difference. What they did not do was determine if the subset of dinosaurs that survived the TJEE had a notable characteristic that could explain their survival.

Until that is shown I think its too early to say "it was just dumb luck". There may have been an advantage amoung the survivors (which may have only been a small % of the pre-Jurassic dinosaurs) that allowed them to survive. Or perhaps it truely was dumb luck.

Either way its too early to conlcude one way or another.

Much to my surprise, this article has lead to a great deal of acrimonious postings on one of my favourite blogs, Sandwalk. To my eye (which, to be honest, isn't the most knowledgeable about the finer details of evolution) the arguments seem to be centred mostly on the definition of what qualifies as "luck".

Saturday musings about data management

2008-09-13T13:11:00.003-04:00

So last week I read a series of articles in Nature about how some science projects, who generate huge amounts of data, are working on solutions to deal with those gargantuan volumes of information.

The scale of data management that some scientific programs involve is mindboggling - they measure data volumes not in gigabytes, not in terrabytes, but in pentabytes!!!

Holy shit batman!

The real depressing part - I have data management issues of my own. On the average day I'll generate between 800Mb and 2Gb of image data. After running those images through my matlab analysis routines I end up with about double that.

My "data management routine" involves nothing more then waiting until the laptop is nearly full, and then transferring the older files to an external hard drive - manually. No cataloguing of the files, no way to "mine" the data.

I suspect that all-to-soon that'll have to change. Unfortunately, despite the rather dramatic cover, Natures series of articles did little to help. No recommendations or methods that would be implementable on my scale, no discussion of software that could be used. So until I decide to startup my own google-like database I guess I'm on my own.

No longer anonymous...and a bit of science humour.

2008-09-10T14:48:00.006-04:00

So John Piere, the man behind the Blog Thoughts in a Haystack, went and ruined everything and announced my existence to the world. Farewell anonymity...and I guess I need to come up with something witty to write about.

I've drawn a blank, so instead of something witty I now present to you my rambling thoughts on the need for more humour in scientific discourse. Now I'm not saying that science and scientists are without humour; in many ways we're rife with it - for example, at the last conference I attended someone (who shall remain nameless) had the witty little snippets "as you know mitochondria are bags of apoptotic factors that occasionally make a bit of ATP".

OK, if you laughed at that you should hang your head in shame. But at least ~~I made an effort to lighten up the mood~~ the anonymous person tried...

But seriously, science humour has a few things to its credit - like common sayings:

When I was your age Pluto was a planet.

Pickup lines:

If I were an enzyme I would be DNA helicase so I could unzip Your genes.

(sorry ladies, I'm taken).

Even our own comic.

But that's not where I think we are humour deficient. Where humour is needed is in the scientific literature. I mean, look at this stuff:

In complex multicellular organisms, cells travel considerable distances through many microenvironments where numerous chemoattractants are encountered. For example, during a host response to bacterial infection, neutrophils must first respond to 'intermediary' cues from endogenous chemokines expressed by endothelial cells in the vasculature and by sentinel cells such as macrophages and mast cells in the interstitium. These signals lead the neutrophils into the general vicinity of the bacteria. Ultimately, the neutrophils must disengage from the intermediary chemoattractants and migrate unidirectionally toward the bacteria-derived 'end-target' chemoattractants

Who the hell writes that stuff? Err wait, I wrote that stuff.

I'm sorry.

Now here is someone who's got the right idea. I don't know how Arthur got this by the editors, but Kudos to him. Quite possibly the best protein structures I've seen in a while.

Exhibit A (err, c): Is it a protein, or is it the G-cleft? Who knows; all I know is those are the keys on the piano you usually play with your right hand.

Exhibit B (err, a): What came first, the membrane-associated egg, or the trans-membrane chicken? And why are they wearing Christmas lights?

Anyways, that's all I got. I guess I should get back to the never-ending search for a paper worth of being presented in journal club - by which I mean a paper I can explain first thing on a Monday morning...

Sometimes I Just Don't Get It

2008-09-09T08:53:00.002-04:00

So a paper came out this Friday in Nature Medicine, looking at the formation of of a neutrophil extracellular trap (NET, image on the right); DNA extruded from a type of immune cell called a neutrophil in order to capture, and destroy, bacteria.

Two things made this new paper unique:

1) They found NETs being formed by another cell type - this time an immune cell called an eosinophil was producing the NETs (I guess eosinophil extracellular traps should be EETs, but that doesn't roll of the tounge, so I'll just call them NETs).

2) They identified the source of the DNA - mitochondria; our cells energy-generating stations.

Both of those observations are quite cool; I'm particularily interested in the mitochondria bit, as my current research deals specifically with mitochondria.

But this is what I do not get - this paper is essentially a "me too" paper, where a group has reproduced another groups published research, with a slight modification (in this case, using eosinophils instead of neutrophils). In fact, this study is almost figure-to-figure identical to one published just last year by my former PhD supervisor. And while having reproducable results is quite important, I'm not too sure how a "me too" paper makes it into such a high ranking journal. I've rejected works (and had my own works rejected) that had more novel data, in lesser journals.

Maybe its an old-boys club, maybe its good luck, maybe I'm missing something in the paper thats super-important, but regardless - I am baffeled. And I wish I knew their secret...

BTW, the image of the NET is from Science Signaling. I hope they don't mind me borrowing it.

Isn't this sexism?

2008-09-08T10:35:00.002-04:00

So I haven't done any HIV research in a few years, and am not the most up-to-date on what is going on. Which is why I'm about a month late blogging on this.

So, as many people may have heard, circumcision can reduce HIV infections by upto 65% in men. Yes, that's right - 65%; nearly 2/3rds of HIV infections ib men (or, approximatly 1/3rd of all HIV infections) could be prevented by simply slicing off the foreskin. Which means that circumcision could represent a huge (and cheap) step forward in controlling the HIV epidemic in regions where the disease runs rampart.

You'd think HIV researchers would be ecstatic about that, wouldn't you?

Most are, but some are are not; the reason - circumcision only helps men. That's right, individuals like Marge Berer, editor for Reproductive Health Matters, has publically stated that we souldn't persue this route as it doesn't help women immediatly. That's right - we shouldn't use an effective preventative measure because it only helps one sex!

Could you imaging the contreversy if someone suggested that we not use pap smears, as they only benifit women in the detection of HPV (which also causes cancer in men).! But the opposite response, one where a therapy is excluded because it benifits primarily men, is bad.

Give me a break - HIV is killing millions, no vaccine or cure is on the horizon, and the infection is spreading faster today than ever before. This isn't the time for ignorence and sexism, in the disguise of political correctness. This is the time to agressivly target the disease with every tool we have; even if some of those tools only help a portion of potential patients.

Yep, sometimes even scientists can be stubid.

Who woulda thunk it? MMR Doe Not cause autism!

2008-09-04T10:17:00.002-04:00

So a new study is out in PLOS One, a leading scientific journal. This new study took an indepth look at MMR vaccination, gastrointestinal (GI) issues and autism. And guess what - no link was found!

The full study can be found here (for free), click on them images below for full-sized figures.

This whole study surrounds a common claim in the anti-vax movement; that the MMR vaccine allows viral entry into the GI tract, leading to autism and the GI issues experienced by some autistics.

The first thing they looked for was virus in the intestine. And surprise, surprise, it wasn't there (see figure below).

Next, they looked for an association with GI problems. And once again, no association was found (see figure below).

Lastly, they looked for a link to the onset of autism, and once again there was no link found (see figure below):

So there you have it - no link. This won't come as a surprise to many scientists; this is about the 10th time this very issue has been analyzed.

But I'm sure that the anti-vaxers are already preparing their counter-claim. And, as per usual, I'm sure that conspiracy will feature strongly in that claim. Afterall, when you have no data, lies and distortions are about all you have left.

It continues...

2008-09-03T12:27:00.002-04:00

So apparently Eppendorf's new add is not a new thing; in fact, Bio-Rad put out this music video a few years ago, advertising a PCR device.

And here I had hoped that eppendorf's video would be one of a kind...

This goes a little too far...

2008-09-03T12:03:00.002-04:00

So eppendorf has a new robot for sale, one which pipettes. As someone who pipettes a lot, this is of some interest (although I don't think the boss will spring for a multi-thousand dollar machine just because my wrists get sore).

Regardless, eppendorf came up with a marketing stratagy for their new robot which is either brilliant or incredibly stupid. They made a music video, boyband style, to advertise their robot. they've got a video, an MP3 and even the lyrics are available for those who want to sing along (please don't).

Pipetting all those well-plates, baby, sends your thumbs into overdrive
And spending long nights in the lab makes it hard for your love to thrive

What you need is automation, girl, something easy as 1 2 3
So put down that pipette, honey, I got something that will set you free

And it’s called epMotion (whisper: ‘cause you deserve something really great)
Girl you need epMotion (whisper: yeah girl it’s time to automate)
It’s got to be epMotion (whisper: no more pipetting late at night)
Only for you epMotion (whisper: girl this time we got it right)

DNA
RNA
Proteins
Cell Cultures
Less reagents
Faster workflow
Saves you money
Well, well, well

And it’s called epMotion (whisper: ‘cause you deserve something really great)
Girl you need epMotion (whisper: yeah girl it’s time to automate)
It’s got to be epMotion (whisper: no more pipetting late at night)
Only for you epMotion (whisper: girl this time we got it right)

There is no contreversy

2008-09-02T12:12:00.005-04:00

So I've been browsing some of the creationist videos on youtube, and am surprised at the consistency of the "teach the controversy" theme in their videos. But I ask - what controversy?

According to the creationists there is some sort of scientific debate as to the reality of evolution. Strange, that in the 12 or so years that I've worked as a biologist that I've not run into it. You'd think that if such a controversy existed that one of the hundred or so scientists I've worked with and known would have mentioned it, or that it would have come up in one of the many scientific meetings I've attended, or that reviewers would have dinged me for not mentioning it in my papers where evolution was featured as a mechanism, or for that matter, that it would have come up in one of the thousands of scientific papers that have crossed my desk.

I've been digging deeper into this "controversy", and I've found - like almost all creationist claims - that this one is a total and complete fabrication of the creationist movement.

But, lets start at the beginning (sorta). Much of this claim comes from the Discovery Institutes "dissent from darwin" project. Basically, this is a list of "scientists" who have signed a rather dubious statement about evolution

We are skeptical of claims for the ability of random mutation
and natural selection to account for the complexity of life. Careful
examination of the evidence for Darwinian theory should be
encouraged.

Seems sensible, doesn't it. Shouldn't any good scientist support examination of our theories?

The problem here is four-fold.

Mutation is not random. Indeed mutations occur preferentially in some regions of the genome compared to others. What "random" means when biologists use it in the above fashion is that the effects of mutations are not biased towards either beneficial or detrimental traits. In fact, the vast majority of mutations are neutral - they provide neither benefit, nor cost, to the organism.
Evolution involves far, far, far more than mutation and natural selection, so the above statement is, in fact true. Of course when you consider the whole of the evolutionary process - hereditary and variation of traits, mutation, recombination, horizontal gene transfer, drift, natural selection, sexual selection, group selection, gene flow, polyploidy, and so forth, the theory of evolution can more than account for the complexity of life.
We already are testing evolutionary theory - to the tune of more than 60,000 scientific research papers a year in the biological sciences alone. How much more do you need?
This is a big one - science no longer follows Darwins evolutionary theory. He had a lot of things right, but not knowing about genes and so forth means that Darwins theory is full of holes. Today we use the new synthesis model of evolution, which takes into account pesky things like genes, mutations, DNA and whatnot. Why the discovery institute thinks that errors in a theory discarded over 60 years ago has anything to do with todays evolutionary theory is . . . well about what I'd expect from DI. Stupidity is their forte afterall.

You'll also notice that I put "scientists" in quotes. The reason for that is most of the people that DI lets sign their lists would not qualify as scientists by the usual standards applied. Normally "scientist" is reserved for someone who:

Has a PhD in one of the hard scienes (biology, physics, chemistry, astronotmy, geology, etc)
Is activly involved in scientific research

The DI list (PDF) is much more broad, for example:

Étienne Windisch Ph.D. Engineering
Mary A. Brown DVM (Veterinary Medicine)
Jonathan A. Zderad Assistant Professor of Mathematics

Not only that, but there is no followup to demonstrate that the people and their credentials are real; something which has been an issue in the past. Their list has ~400 signatories, but when you filter out all of the people from outside of science the list falls to about half. I don't have enough time to check each and every one of those individuals scientific publications; but a random sample of 25 found 6 pubication from one person, of which zero were on the topic of evolution.

Compare this to Project Steve, a humerous counterpoint to the DI's dissent frm darwin list. This list is much like the DI's list, except that the signees are confirmed to be scientists (by my above definition), AND THEY HAVE TO BE NAMED STEVE.

Despite the rather restrictive conditions to sign, the Steve-o-meter has today 894 signatories, double that of the DI's list (the DI's list has 9 Steve's, of which 5 meet the scientist criteria from above).

About 1% of all scientists are named Steve, therefore the Steve list should represent the opinion of 89,400 scientists. So lets compare:

400-ish signees on the DI's list, divided by 89,400 represented on the steve list = 0.44% of scientists in disagreement with evolution
5 scientists named Steve on the DI list, divided by 894 on the steve list = 0.56% of scientists in disagreement with evolution

Wow, big contreversy, one-half of one percent.

Of course, lists can be altered, fudged, and don't really represent reality. The best insight into the opinion of scientists on evolution can be found in the scientific literature, where we report our findings and thoeries. A google scholar search for evolution in publications from the biological sciences shows 261,000 papers on the topic. The DI was kind enough to provide a list of pro-creation scientific papers on their page.

Contrary to their claims, the papers are not publised in achedemic, peer-reviewed science journals; rather many are books, and only a few of the papers are published in scientific journals. Ignoring the books, and papers appearing in educational or philosophical journals, there are 43 papers listed in their bibliography.

Back to the math:

43 creationist papers divided by 261,000 papers on evolution = 0.0165% of scientific papers in favor of evolution, verses 99.9835% of papers in favour.

Now lets go back to google, but look for all scientific papers on evolutoin; grand-total is 2,700,000.

Some more math:

43 creationist paper divided by 2.7 million papers on evolution = 0.00159% of scientific papers in favour of evolution, verses 99.99841% in favour.

99.99% is not a contreversy; its a complete and total consensus.

On second thought, lets teach the controversy! Showing children that only the teeniest, tinyist portion of scientists believe in creationism would put all of this to rest.

Long weekend roundup

2008-09-02T09:58:00.005-04:00

So the Labour Day long weekend is over. What does a scientist do on a long weekend you ask - the plan was: 1) Do a practise dive (SCUBA), 2) Get groceries, 3) Walk the dog many times, 4) see a show.

Instead I ended up staying home with the flu; luckily it hit before the dive, as I'm out of practise with the warhammer manoeuvre.
Being sick left me with a lot of time to watch the political shenanigans, both here in Canada, and with our friends to the south.

On the home front, we have our conservative PM trying to call an Oct 14th election, despite the fact that last election he campaigned on (and won on) a platform which would create set election dates. Not only did he campaign on that, but he passed a law setting election dates. So he's breaking the law - don't you go to jail for that?

But its not just the conservatives who were idiots over the weekend; Canada's green party just got their first member of parliament - Blair Wilson. Except he wasn't elected, he defected from the Liberal party. I wonder how his constituents feel about being represented by a party who received only 3,966 of the 63,624 votes case (i.e. 6.2% of the popular vote)?

South of the boarder, the US presidential election is beginning to heat up. McCain picked Sarah Palin (Sarah who?) as VP. Almost immediately it was announced that her 17 year-old unwed daughter was pregnant. Quite frankly I couldn't care less, but the response to this news has once again proven my contention that all politicians are scum, without a moral bone in their body.

The conservative right immediatly threw away (or at least ignored) their claims that their "values" prevent stuff like this from happening, that teen pregnancy is a product of rampant liberalism, and all the usual BS they spout, and started congradulating Palin on her support of her daughter! Double standard - you bet. But not to be undone, the democrats tried to make an issue of this, and even going so far as to ask if Palins infant daughter was actually her grand-daughter. Give me a break; since when does the fecundasy of ones daughter determine your effectivness (or lack thereof) in political office.

I used to feel sorry for Americans, for having only two crappy political parties to choose from. I'm not so sure that sorrow is properly placed - afterall, choosing between two pieces of crap parties is probably a lot easier then trying to sort through the 5 piece of crap parties we got up here.

Man, shoulda done some science over the weekend; I may have actually had something fun to blog about if I had...

Ahh, matlab

2008-08-29T18:52:00.002-04:00

Oh, the wonders of matlab. Once upon a time (Tuesday, to be exact) I was in a world of hurt - over 30 multi-colour microscope stack to analyze. For those of you not familiar with microscopy, think of having around 2000 images of a crowd, and having to circle the face of one specific person (who moves image-to-image) in each and every one.

Tedious, yes. Hence why this blog was born (why work when you can waste time on the net?).

Enter Matlab.

A few pages of script, a few borrowed files from others in the lab, and bam - its done. Now, instead of sitting there for hours on end I type analyze_all (directory), and go for coffee.

Computers truely are a wonderful tool.

Lies, damned lies and vegetarians . . . err, statistics

2008-08-28T12:17:00.004-04:00

So the vegetarians are on the warpath again. This time the Physicians Committee for Responsible Medicine - a front for the anti-meat movement have created a project called "The Cancer Project".

The target of this project - hotdogs and children.

And what is wrong with hotdogs, you ask? The answer is not much; while not the healthiest of treats, normal consumption is harmless (aside from your wasteline, of course).

However, if you eat one or more hotdogs each and every day, over a period of many years, you may - and I repeat may - slightly increase your risk of colon cancer. How slight? You would go from an 5.8% lifetime risk to a 7% lifetime risk.

The question, of course, is how truthful are they being. The answer is - as always - not very. Despite the fact that numerous studies have been preformed asking this very question, not one has ever provided a firm answer. Some find no link, while others find weak (usually not statistically significant) links. To make things even more confusing, there are differences between men and women, as well as the region of the colon being analyzed. Oh, and none of the studies looked at kids, so "the cancer projects" use of children in their commercial is inaccurate; they'd be better off showing an obese 50-60 year-old, as that would actually represent the demographic that may be at risk.

But the most damning by far for the pro-vegetarian lobby, and the one piece of data they'll never admit to, is that not one study has shown that a vegetarian diet helps. In fact, at least one study has shown that non-vegetarian diets can help reduce colon cancer risk. For example:

"A significantly reduced risk of distal colon cancer was noted in women only with increasing intake of dairy products and of milk."

Hu J et al. Eur J Cancer Prev. 2007 Aug;16(4):275-91.

And, as always, the vegetarian front has completely failed to mention the hundreds of studies showing the detrimental health effects - from semi-avoidable issues like anemia and decreased immunity, to the unavoidable issues due to the large amounts of phytoestrogens contained in the vegetarian diet. Among the phytoestrogen issues are birth defects in male children, decreased fertility, immunospression, and memory loss.

So what are we to believe? Simple - we've spent the last 6 million years evolving into omnivores, and as a result the best diet for us is an omnivorous one. And, like always, moderation is key. A hotdog once in a while won't hurt you...

Anti-vaccination in action

2008-08-27T09:37:00.003-04:00

So most people are probably aware of the anti-vaccine movement; if you don't their simply a bunch of quacks who claim - in the complete absence of evidence - that vaccines are harmful, do not work, and cause autism. For reasons beyond my understanding, people actually believe them.

And now, we can see the results in action. In British Columbia Canada we've got a nice big mumps outbreak - and 100% of the 200-ish patients are not vaccinated. Yep, they sure are healthier than those of us who've been vaccinated. Swollen glands, male infertility, excruciating pain, and hearing loss are all signs of healthy children.

Well, in anti-vaccine land those are signs of "healthy children", and "normal, harmless childhood disease".

And this is just one of dozens of known cases where diseases re-emerged after vaccinations were stopped.

If only parents would read, instead of just listening to these idiots.

Inaugural Posting

2008-08-26T17:59:00.002-04:00

I doubt many people will see this, but welcome to my blog. I hope that I'll eventually fill this space with stuff people may actually want to read.