Monday, September 29, 2008

Which organisms can feel pain?

I recently tasted raw habanero chili pepper for the first time. Just to give you an idea they rate at about 200 000-300 000 scoville units, compared to say jalapeños which have a measly 4000. This means that you have to dilute them over 200 000 times in sweet water before they stop burning. Needless to say it wasn't a very good idea and I had a near-death experience as my airways swelled so much that I could no longer breathe for nearly a minute. Do not underestimate the danger of hot peppers, they can be lethal. I was surprised to learn that birds can eat said peppers without so much as a sweat. Apparently it is mostly effective against mammals, and birds are immune to capsaicin, which makes for a clever way to get the damn squirrels out of your bird feeder. All of this is simply a segway to introduce another beer-fueled science debate we had at the pub. Is pain sensation limited to mammals? Warm blooded organisms? vertebrates?

You might recall that a while back a (very poorly conceived) paper about fish feeling pain created quite a stir. I suppose it all comes down to your definition of pain. For something we feel so ubiquitously pain's definition is rather elusive. Is it the "discomfort" you feel to a noxious stimulus, is it a reflex as a result of injury, is it the emotional suffering translated by our higher brain centers in response to the stimulus? As somebody who's worked with both fish and rodents I'd be inclined to think that all vertebrates feel pain. In fact by watching how slugs react to a poke, I think they might even be able to feel the essence of it. How else would they have survived this long if they couldn't learn from injuries to stay out of harm's way?

here is what the Wellcome Trust has to say about the subject:

"Nociceptive nerves, which preferentially detect injury-causing stimuli, have been identified in a variety of animals, including invertebrates. Indeed, the leech and sea slug are classic model systems for studying nociception. However, it is believed that invertebrates are capable only of stimulus-response reactions and lack the necessary brain system that vertebrates have to process pain.

In vertebrates, nociceptive information is collated and augmented in the brain and signals are relayed down the nervous system to alter the intensity of pain. All vertebrates possess the primitive areas of the brain to process nociceptive information, namely the medulla, thalamus and limbic system.

However, one area of great importance for pain perception in humans is the cortex and its relative size decreases as we descend the evolutionary tree. For instance, in relative terms, the cortex gets smaller going from humans, through primates, mammals, birds, reptiles, amphibia and finally to fish, which possess only a rudimentary cortex."


Bayblab podcast: Episode20

A new season of the bayblab podcast is back (rss, mp3). As usual we drunkenly ramble about the cancer carnival and specualte on how dogs can smell cancer, we talk about the different classes of substances abused in sports and why it is unethical, we talk about personal genetic information, privacy and companies like 23 and me, and finally we display our ignorance by tackling basic science questions....


Sunday, September 28, 2008

Call for Submissions

The 14th edition of the Cancer Research Blog Carnival is coming up this Friday, Oct. 3 at ScienceBase.

Be sure to get your submissions in here.


Wednesday, September 24, 2008

Varmus on "The Cure" for Cancer

“These are incredibly complicated scenes that we're only beginning to understand thanks to the genome project and spinoffs from the genome project.

“And the hope that advocacy groups understandably have – that if we just do a little bit more research and apply it at the bedside, that we're going to cure cancer – is really terribly simplistic.

“And when scientists give support to that simplistic notion, which they are likely to do because it's the way of raising money, they create an expectation that's very hard to meet.”

...And he argued that the culture of unrealistic expectations is encouraged by the way science is taught in schools, with a focus on outcomes rather than process.

(More at the Globe and Mail)

My question: what proportion of research funding currently goes to BASIC cancer biology research with no obvious "therapeutic/therapeutic target" pay-off?


How far should we go to protect academic freedom?

Noam Chomsky once said "If we do not believe in freedom of speech for those we despise we do not believe in it at all.". I couldn't agree more. See we have this tenured professor at Ottawa U who likes to stir shit, his name is Denis Rancourt. One day he decided to turn his environmental class into an activism class and decided to fight the powers or "speak truth to power" as he likes to say. He decided to get rid of the grading system and give A+ to everyone because grading maintains an oppressive class system that legitimizes the heredity of the rich elite. I personally would have been pissed if it had been my class and I was genuinely interested in learning about environmental chemistry, but certainly don't oppose those ideas being taught on his and his student's own time. He then practiced what is known as academic squatting (link to his blog) to show political documentaries and invite speakers and allow both students and the public to be exposed to those ideas in the university's space. Finally he put up a website whose sole purpose is to document anything that would be suspicious about the university called UofOwatch. In short he stirred shit.

Of course the university blew a fuse, he was stripped of teaching duties, cannot mentor graduate students, all the lawyers went after his UofOwatch site for libel and copyright infringement, and they tried to shut down his cinema night because it didn't include access for the deaf. See this is where the university failed to do the right thing. Yes he shouldn't be teaching activism in a chemistry class, yes it is inappropriate for him to have graduate students, because he doesn't do research but why make a martyr out of him. What's wrong with debating ideas and exposing students and the public with controversial political thoughts, what's wrong with criticizing the administration. If they had legitimized him instead, well he would've been largely ignored anyways, and the university could have taken the moral high ground. Instead we are at risk of losing academic freedom and the role of universities to promote free speech and discourse.

See that's the kicker, I don't agree with anything I've ever heard coming out of his mouth: I don't think global warming is a plot to keep the masses in fear, I don't think corporate interests control all academic research, I don't think chemotherapy has never been proven to work, I don't think tenure forces professors to turn into sheep, I don't think higher education stops us from thinking on our own, but goddamn it I do think he should be allowed to proclaim those ideas without being muzzled. Because if we don't let this professor criticize our university and expose his cockamamie ideas, then when somebody comes with something important to say we wont be able to hear them. So I appeal to you Mr. A-ROCK, someone I admire a great deal more than Denis, do the right thing. Remember the days when you organised peace conferences and brought Lennon to Canada, or when you came within a smidgen of passing the pot legalisation law as a justice minister? I want that guy back as my university president.


IA updates

Some new IA posts for those who dabble in reading not just science geek blogs (bayblab) but IT geek blogs aswell. Broaden your geekness! Lots of stuff on digital privacy and free speech and the usual collection of 'Fun Stuff' including a Swedish Funiture Name Generator.


Tuesday, September 23, 2008

Urine match heads

We discussed at lunch if you could survive, drinking your own urine. It was lunch so drinking other people's urine wasn't discussed as it seemed unappetizing.
In any case I can't really figure out how long you could repeatedly drink your own urine to stave off dehydration. However you could distill your urine. Of course, I wouldn't bother with digging a pit ect. like the link suggests when you could just do it on your stove.
In any case this reminded me that urine contains the element phosphorus, which has an interesting history. Check out a great synopsis on the history the discovery of phosphorus. Also there is an entire book out about phosphorus. Here is a review of The Shocking History of Phosphorus by John Emsley by the Naked Scientists.


Monday, September 22, 2008

Quack hunting season is open - update

We've talked about how the US authorities have finally started cracking down on bogus cancer cures, including abroad. The FTC has also built a new website to try and warn potential customers about misleading claims and potential hazards of alternative therapies by giving helpful advice:

"# Natural doesn't always mean effective. Scammers take advantage of the feelings that can accompany a diagnosis of cancer. They promote unproven – and potentially dangerous – remedies like black salve, essiac tea, or laetrile with claims that the products are both “natural” and effective. But “natural” doesn’t mean either safe or effective when it comes to using these treatments for cancer. In fact, a product labeled “natural,” can be ineffective and even downright harmful.
# Bogus marketers often use trickery and vague language to take advantage of people. Testimonials on websites with ads for products that claim to cure or treat cancer can seem honest and heart-felt, but they can be completely fake: in fact, they may not disclose that actors or models have been paid to endorse the product. Even when testimonials come from people who have taken the product, personal stories aren’t reliable as evidence of effectiveness."

You can also report bogus cures straight to the FDA, and I know just the one who has been asking for it... Well the list has finally been made public and it includes such gems:

"Alexander Heckman d/b/a Omega Supply – Among the products this company marketed are laetrile, which can cause cyanide poisoning when taken orally at high doses; hydrazine sulphate, which is classified by the U.S. Department of Health and Human Services as a potential carcinogen; and cloracesium, which contains celsium chloride. According to the complaint, in addition to making deceptive and false claims that these products are safe and that they effectively prevent, treat, and cure cancer, the respondents also made false claims that the products are scientifically proven to work.

Native Essence Herb Company – The products marketed by this company include herbal concoctions (Rene Caisse essiac tea blend and cat’s claw), the herb chaparral, and maitake mushrooms extracts. In 1992, the FDA classified chaparral as unsafe because of its “association with acute toxic hepatitis.” According to the complaint, the respondents made deceptive and false claims that these products are effective for treating and curing a variety of cancers, eliminating or shrinking tumors, and for preventing breast cancer."

Now come and tell me this industry doesn't need regulation...


Saturday, September 20, 2008

Grave-robbing for Science

The Spanish Flu killed an estimated 20 to 100 million people across the globe in the years 1918-1920. Towards the end of the pandemic soldier and diplomat Sir Mark Sykes was killed by the virus and buried in a lead coffin.

With lingering fears of a possible bird flu (H5N1) pandemic, and with a dearth of samples from Spanish flu (a subtype of avian flu H1N1), he has recently been exhumed by scientists -- paging Dr. Frankenstein!

Taking tissues from his body, well preserved by his lead casket, the team is trying to learn more about the Spanish flu and how it killed him in the hope of transferring that knowledge to the understanding and treatment of H5N1. His body was re-interred after removing samples in a special laboratory, airtight to avoid any risk of contamination.


Friday, September 19, 2008

The Evolution of Assholes

No, I don't mean Denis Leary. In an article in Nature [Nature News summary], two scientists from the University of Hawaii try to tackle the burning question of the origin of the anus.
Today, two evolutionary biologists have published genetic evidence in Nature that they claim refutes the leading theory of anal evolution. Their work suggests that the anus may have evolved multiple times in many different organisms, and they propose that, in some lineages, the anus may have formed through a fusion of the gut with the reproductive organs.
Current theory holds that in early organisms with one hole (a mouth used for both eating and excretion - imagine the aftertaste!) the mouth eventually separated into two orifices, one of which gradually to migrated to the opposite end (anus next to the mouth? - imagine the smell!).

The new study examined developmental gene expression patterns in worms. They found that in both worms with one 'hole' and those with both a mouth and an anus, the same genes were involved in forming the mouth. However anus-forming genes were different, contrary to what would be expected if the anus branched off from the mouth. Similar 'backside' genes were also expressed at the posterior of the no-asshole worm - one of them in the reproductive tract. This led to the suggestion that rather than branching from the mouth, the reproductive organs may have evolved first and then joined with the gut - think cloaca.


Thursday, September 18, 2008

Science and polittics: Canadian elections

While the world watches the run-up to the US election in a background of near economic collapse few noticed that Canadians will also go to the polls this fall. Canadian's themselves seem to be paying attention to the south more than their own backyard (66% favor Obama, 14% McCain). While there was some coverage of science issues in the US election we have yet to hear much about it in Canada. A quick look at the campaign sites of the 5 major parties shows that all focus to some degree on global warming but don't delve much deeper. Liberals are pushing their "green shift" but don't pay much attention to other science issues. Conservatives don't seem to have a definite plan but like to boast about their environmental record. The NDP mentions both environmental protection and the increasingly popular cap-and-trade system. The green party is not-surprisingly the most thorough. The Bloc Quebecois have a nice video.

So over the next weeks we'll try to see how the different parties stack up on science issues. Yes the environment is a particularly pressing one, but there are many others: science funding, reinstating a scientific advisor etc...

leave it to Nature, a British journal, to have the best editorial and news on the issue so far...

follow the link for more reading:

Indeed, many Canadian scientists are seeing, and complaining about, an undue emphasis on commercially focused research over long-term basic research. Such complaints are heard in many other countries too. But in Canada the problem is compounded by the fact that the current government has channelled new science funds into four restrictive priority areas — natural resources, environment, health and information technology — and that scientists are often required to scrounge matching funds from elsewhere to top up their grants. Furthermore, the government this month defined sub-priority areas that mix in obvious commercial influences: alongside 'Arctic monitoring', for example, sits 'energy production from the oil sands'.


Trans-splicing and Chromosomal Translocations

I'm up for the research group journal club tomorrow. Since a couple of the bayblab readers will not be able to make it, I thought I'd pass on what I'll talk about.
A recent publication in Science, demonstrates that an mRNA in a normal endometrial cells encodes the exact same fusion protein that normally occurs as the result of a translocation found in 50% of endometrial cancers. The transcript, as detected by RT-PCR and RNase protection assay is found in abundances that are affected by hormone treatment and hypoxia, suggesting that it has a biological role. In cancer this fusion protein results in resistance to apoptosis and increased proliferation. However, in theses normal cells, there is no DNA encoding for this hybrid mRNA and the authors suggest it is a result of trans-splicing. Trans-splicing of this sort has not been observed in vertabrate cells and even in other organisms it is quite different.
They go to great pains, of course, to demonstrate that it is not an RT-PCR artifact and that there is not a subpopulation of the normal cells that contain the translocation.
The killer is that they do in vitro trans-splicing assays using Rhesus and Human nuclear extracts and indeed find this chimeric mRNA. I'm sure they are looking for other fusion mRNAs using this assay in a high throughput method.
This study raises some intersting question about these oncogenic fusion proteins that are very common in cancer. Particular fusion proteins are repeatedly found in particular cancers. Do they have a function in normal cells? Is it through the mechanism that produces these mRNAs or the mRNAs themselves that cause these cancer associated translocations??
At least check out the figure. Translocation is indicated in the centre of the figure. Two mRNAs combine to create a novel one that has no DNA equivalent.


The origin of evolution

I found this rather neat paper in PNAS on how natural selection and evolution actually predate the origin of life. If you assume that to be alive you must require the conditions of being able to replicate and evolve, than you have to wonder which came first. According tho their model, not only did abiotic information systems undergo natural selection but evolution favored the emergence of replication. It's a short read if you understand mathspeak (which I don't), but here's the gist of it from the concluding paragraph....

Traditionally, one thinks of natural selection as choosing
between different replicators. Natural selection arises if one type
reproduces faster than another type, thereby changing the
relative abundances of these two types in the population. Natural
selection can lead to competitive exclusion or coexistence. In the
present theory, however, we encounter natural selection before
replication. Different information carriers compete for resources
and thereby gain different abundances in the population.
Natural selection occurs within prelife and between life and
prelife. In our theory, natural selection is not a consequence of
replication, but instead natural selection leads to replication.
There is ‘‘selection for replication’’ if replicating sequences have
a higher abundance than nonreplicating sequences of similar
length. We observe that prelife selection is blunt: Typically small
differences in growth rates result in small differences in abundance.
Replication sharpens selection: Small differences in
replication rates can lead to large differences in abundance


Tuesday, September 16, 2008

Worm therapy

Leeches and maggots have a history of use in medicine - for blood-letting or wound cleaning, respectively (and both have FDA approval for modern medical use). Recent reports have suggested potential usefulness for another creepy-crawly.

Filarial nematode worms are particularly nasty mosquito-borne parasites that take up residence in the lymph nodes. The worm is endemic to many tropical and sub-tropical countries and causes elephantiasis - the enlargement of limbs and genitals (and for guys thinking this doesn't sound so bad, the genitals can get so big that they interfere with regular physical activity. Pictures here), as well as less obvious internal damage. However, areas with high rates of filarial worm infection tend to have lower rates of inflammatory bowel disease, arthritis and other inflammation-caused ailments. This is thought, in part, to be caused by ES-62 - a glycoprotein secreted by the worm that has anti-inflammatory properties.

Scientists in Glasgow are now looking for a way to develop ES-62 into a better, non-heart-attack-inducing, anti-inflammatory.

Don't worry though - I don't think they plan on treating with live worms.


RFF: red fluorescent fish

On the upcoming podcast we explain amongst other things why the sea is blue and what happens to red light in water (subscribe to the rss to listen!). For depths over 10m red light is pretty much irrelevant to fish. There is no purpose to see it since it is largely absent, and therefore no value in displaying it. Or is there? Here is a paper in BMC ecology with some stunning pictures and an account of how actually not only are some fish red-fluorescent, but it is also a really good private communication solution:

"We here report that at least 32 reef fishes from 16 genera and 5 families show pronounced red fluorescence under natural, daytime conditions at depths where downwelling red light is virtually absent. Fluorescence was confirmed by extensive spectrometry in the laboratory. In most cases peak emission was around 600 nm and fluorescence was associated with guanine crystals, which thus far were known for their light reflecting properties only. Our data indicate that red fluorescence may function in a context of intraspecific communication. Fluorescence patterns were typically associated with the eyes or the head, varying substantially even between species of the same genus. Moreover red fluorescence was particularly strong in fins that are involved in intraspecific signalling. Finally, microspectrometry in one fluorescent goby, Eviota pellucida, showed a long-wave sensitivity that overlapped with its own red fluorescence, indicating that this species is capable of seeing its own fluorescence."

Not only is this cool in itself but it may be useful for us lab rats to use in imaging and microscopy as it would have different properties than RFP and current dyes.


Thursday, September 11, 2008

Iron Maiden and "Déjà Vu"

In a recent Nature Podcast (I think?) I heard a short interview with the blogger running Mind Hacks who was attending the first European science blogging conference . He mentioned that his favorite post was this story about Iron Maiden lyrics being cited in a paper as a description of deja vu. I just had to share the paper and lyrics:

here is the paper that started it all:
the déjà vu experience is a subjective phenomenon that has been described in many novels and poems. Here we review over 20 literary descriptions. These accounts are consistent with the data obtained from psychiatric literature, including various phenomenological, aetiological and psychopathogenetic aspects of the déjà vu experience. The explanations, explicitly formulated by creative authors, include reincarnation, dreams, organic factors and unconscious memories. Not infrequently, an association with defence or organic factors is demonstrable on the basis of psychoanalytic or clinical psychiatric interpretation. The authors recommend that psychiatrists be encouraged to overstep the limits of psychiatric literature and read prose and poetry as well.

And somebody submitted these lyrics as a comment in the British journal of psychiatry quoting the song:

When you see familiar faces
But you can't remember where they're from
Could you be wrong?

When you've been particular places
That you know you've never seen before
Can you be sure?

'Cause you know this has happened before
And you know that this moment in time is for real
And you know when you feel déjà vu.

Feels like I've been here before (rpt. four times)

Ever had a conversation
That you realise you've had before
Isn't it strange?

Have you ever talked to someone
And you feel you know what's coming next
It feel pre-arranged.

'Cause you know that you've heard it before
And you feel that this moment in time is surreal
'Cause you know when you feel déjà vu


You can listen to it here...


Wednesday, September 10, 2008

IgNobel candidate?

Leaked to the bayblab from our very own ottawa/hull patent office. Now I have fully restored the poo/sex content to the bayblab:

My product is a device composed of a cotton like material it is cylindrically shaped and bears small perforations whereby an agreable scented powder or perfume may exute it's odor.
My product bears roughly the same dimensions of "TAMPON".
My product is went to be wedged between the cheeks of the buttock.
My product illiminates anal itching due to sweat accumulation and residual of human excrement due~~~~ improper or insuffient wiping of the anus after having gone to the washroom.
My product absorbs excess anal sweat, creates a dry comfort zone
My product illiminates embarrassing flatulance sounds.


Monkey news

Those of you who've listened to Ricky Gervais' podcast in the past might understand why monkey news was my favorite section. I've always had an uneasy fascination with monkeys and great apes. On the one hand I find it amazing that these species are so close to us, and I marvel at their behaviour and what it can teach us about ourselves. On the other hand I'm suspicious of anything that may be related to us. In fact I fear great apes more than I would fear a lion, because both can physically overpower me, but the ape may actually be able to outsmart me too.
One topic we've discussed in the past is human rights and whether they should apply to our closest cousin. I find mildly amusing that we try to download our values to other species, when even amongst human societies we can't agree on universal rules. I know monkeys and apes have a sense of fairness, but do they have a sense of morality, and does that even make sense to non-human animals. So keep that in mind as you explore the links of monkey news:

1) The first is a rather graphic video of a love affair between a chimp and a frog. Most people I've shown this to reacted rather strongly to it. If you can't watch it, I might point out that the frog looks rather unharmed even if it might not have been quite consenting. My question is : is this depravity. Is the chimp doing something wrong?

2) I'm always surprised that more people don't know about the bonobo societies and their "make love not war" attitude. Unlike their more violent cousins the pan troglodytes (who wage wars, and uses spears) the bonobo (pan paniscus) resolve conflicts within a group mostly via bonding from sex. I'll forever have the images imprinted on my mind of the video I saw in high school biology showing chimp orgies which included masturbation, oral, homosexual, pedophilia and incest. A recent report shows that chimps also like hugs: "The research is said to provide the first evidence that consolation in primates, such as hugging and stroking, can reduce stress levels after a fight. The behaviour could indicate some level of empathy, Dr Orlaith Fraser told the British Association Science Festival."


Tuesday, September 09, 2008

Poo Identification

It's been some time since we had a scatalogical post - which is odd considering how often it comes up at lunch. Last month, Adventures in Ethics and Science had a "name that poo" challenge, calling on readers to identify the feces of several circus animals. Check it out and tell us how you did. Use this flowchart if you must. Answers are here. No cheating!


Monday, September 08, 2008

LHC's first beam on Wednesday...

If you're reading the bayblab you're probably as excited as us about the LHC getting switched on this week (and maybe you have that tune in your head). Well the good news is that you'll be able to watch it live in a webcast. And in the odd chance that the doomsday sayers were right, you'll have front seats to the apocalypse. For folks in Ottawa the show should be on at 3:00 AM on Wed. For others check here.


Friday, September 05, 2008

Cancer Carnival #13 at Highlight HEALTH

The 13th Edition of the Cancer Research Blog Carnival is now up at Highlight HEALTH. Lots of cancer research goodness as usual.

And don't forget to check out the carnival's new homepage (now with easy-to-add RSS Feeds!) and sign up to host the next one!


Stand Up To Cancer

Tonight at 8pm, ABC, CBS and NBC (the big three US TV networks) will denote 1 hour, commercial free, to a star-studded fundraising campaign: Stand Up To Cancer. The goal of this initiative is to raise money for cancer research. Of the money raised, 70% will go to 'Dream Teams' - multi-institutional translational and clinical research teams - and 20% will be designated for "innovative, high-risk research proposals". This money will be administered by the American Association for Cancer Research (AACR). The remaining 10% will be used as an endowment to sustain the Stand Up To Cancer program and to fund unexpected research opportunities.

In addition to the network event, YouTube is getting in on the action. The frontpage currently features Stand Up To Cancer videos and donations can be made through the site.


Thursday, September 04, 2008

Early Cancer Detection: Dogs with frickin' laser beams

You may recall from several years ago, reports of dogs who could sniff out cancer. Based on odour, trained dogs could distinguish urine from bladder cancer patients from controls at a better-than-chance rate (mean success rate of 41% vs. 14% expected by chance alone in this study).

Since then, more canine cancer detection experiments have been done. In 2006, this double-blind study showed that ordinary household dogs could be trained to identify breast- and lung-cancer patients with incredible accuracy (88% and 99% respectively) and specificity (98% and 99% respectively) compared to conventional diagnosis and biopsy confirmation, based on breath scent. The dogs were able to 'diagnose' both early- and late-stage cancers.

Fast forward to 2008. While a Korean company is cloning cancer-sniffing dogs, a group at the University of Oklahoma - intrigued by the dogs, and having already published proof of concept to identify volatile compounds in breath - announced a project to develop a tool for laser-based detection of cancer biomarkers. The goal is to eventually develop an 'electronic nose' for rapid, accurate, non-invasive cancer diagnosis.
According to McCann, “Improved methods to detect molecules have been demonstrated, and more people need to be using these methods to detect molecules given off from cancer. We have developed laser-based methods to detect molecules. Mid-infrared lasers can measure suspected cancer biomarkers—ethane, formaldehyde and acetaldehyde.” McCann will use nanotechnology to improve laser performance and shrink laser systems, which would allow battery-powered operation of a handheld sensor device.
Because of the importance of early detection, this device - if sensitive enough to detect early-stage cancers with a simple breath test - could have major implications for survival rates. Unfortunately right now it's just a press release and, as pointed out in the release, an actual product is 5-10 years away, but in the meantime more biomarkers can be investigated and more cancers can be screened as candidates for laser-based diagnosis. As McCann states, "the science supports it, and the dogs tell us there is something there."


Tuesday, September 02, 2008

Science Poll

By a show of hands, would you rather:

- Keep working on a problem even if you might never find the answer, because you like the pleasure of figuring things out yourself.

- Be given the answer to your problem that has eluded you for awhile, even if it means you'll have to admit defeat and work on something else.



Monday, September 01, 2008

Where does life hide when the meteor strikes?

Deep trenches in the ocean? Underground cave systems? Amazing...