Your turn 10C, 10D,
Problems 10.1, 10.4
Due this friday (late policy up to Wayne, who by elimination is the one marking them).
-Seth
Monday, 24 October 2011
Saturday, 22 October 2011
Presentation Marking Criteria
This is the marking criteria from PHYS3900 presentation, I think it's general enough to be used to grade our presentations.
Thursday, 20 October 2011
Integrate-and-fire
The integrate-and-fire model of neural networks followings on nicely from my last post and also ties in with the subject of the next chapter. It's a phenomenological model of neurons which "integrates" the depolarizations incident on a neuron's cell body and "fires" an action potential down the axon when the depolarization reaches the threshold value. Often additional time dependent exponential decay terms are added to better replicate observed behaviour; when calibrated carefully this model is a cheap and robust method of investigating neural networks.
While integrate-and-fire doesn't allow for the investigation of temporal encoding, it can be used to model large neural networks and captures some of the effects of combining analogue and digital signals along with the topological structure in the network. It is a model liked by many computational neuroscientists and disliked by biologists a physicists in equal measure (just for different reasons).
For more details see: A review of the integrate-and-fire neuron model: II. Inhomogeneous synaptic input and network properties.
While integrate-and-fire doesn't allow for the investigation of temporal encoding, it can be used to model large neural networks and captures some of the effects of combining analogue and digital signals along with the topological structure in the network. It is a model liked by many computational neuroscientists and disliked by biologists a physicists in equal measure (just for different reasons).
For more details see: A review of the integrate-and-fire neuron model: II. Inhomogeneous synaptic input and network properties.
Wednesday, 19 October 2011
I have detected James' draft post on shrimp circularly polarised light detection: I have a National Geographic at home which says a particular species of shrimp can detect something around 21 wavelengths/polarisations of light. Quite impressive...
Another group from BIOL1040 that I asked questions of had found research on the different spectra that primates can detect. Humans are generally trichormats (3 frequencies + rods), as are most Old World primates (and most marsupials) whereas except for Howler Monkeys, New World primates and most other mammals are dichromats (2 frequencies + rods). The interesting bit about New World primates is that their gene structure allows females to be trichromats whilst males are dichromats. This occurs because the gene for red and green colour sensing (blue/violet apparently was the first type to develop) occupies the same locus (i.e. spot) on the NW primate X-chromosome, so females can have both genes (one on each X chromosome) and are trichormats (unless they recessively possess only the same gene on both X chromosomes) but males can only ever possess one of the genes (on their single X chromosome). Howler monkeys are thought to have re-developed trichromatic vision from gene duplication; apparently mammals in dinosaur times were tetrachromats (could see 4 colours). The evolutionary reason for this unusual set-up in NW primates was suggested to be that darker conditions favour dichromatism (it's better in low light conditions, apparently) whereas in lighter conditions, trichromatism is more useful (you can tell the differences between fruits, for example, or between paintings, local creatures of the Amazon)—communities of primates of one species can therefore utilise all of the members' vision ranges to the group's advantage. I was a little skeptical about this point, however, as I don't really see why trichromatism is a disadvantage in low light conditions; surely low light sensitivity is more dependent on rods and eye structure?
An analysis of the wavelengths of the opsin pigments would be interesting. I must also remember to post another BIOL1040 response on eye structure and detection pigments (e.g. opsin) in cubozoans (i.e. box jellyfish) compared with other lineages (e.g. vertebrates).
Other interesting visual patterns include lungfish, which see four wavelengths, bees, which see UV, green and blue, and many bird species in which juvenile members see four wavelengths but adults only see three or two.
Then there are crustaceans....
Also, an interesting thing I read in a Scientific American concerned the human brain's way of interpreting colours. Apparently, we see in a blue-yellow channel and a green-red channel, preculding the existence of greeny-reds and bluey-yellows. Unless you torture a subject's poor brain for some time. I may have to search for the issue, I read it in a doctor's surgery some time ago....
Another group from BIOL1040 that I asked questions of had found research on the different spectra that primates can detect. Humans are generally trichormats (3 frequencies + rods), as are most Old World primates (and most marsupials) whereas except for Howler Monkeys, New World primates and most other mammals are dichromats (2 frequencies + rods). The interesting bit about New World primates is that their gene structure allows females to be trichromats whilst males are dichromats. This occurs because the gene for red and green colour sensing (blue/violet apparently was the first type to develop) occupies the same locus (i.e. spot) on the NW primate X-chromosome, so females can have both genes (one on each X chromosome) and are trichormats (unless they recessively possess only the same gene on both X chromosomes) but males can only ever possess one of the genes (on their single X chromosome). Howler monkeys are thought to have re-developed trichromatic vision from gene duplication; apparently mammals in dinosaur times were tetrachromats (could see 4 colours). The evolutionary reason for this unusual set-up in NW primates was suggested to be that darker conditions favour dichromatism (it's better in low light conditions, apparently) whereas in lighter conditions, trichromatism is more useful (you can tell the differences between fruits, for example, or between paintings, local creatures of the Amazon)—communities of primates of one species can therefore utilise all of the members' vision ranges to the group's advantage. I was a little skeptical about this point, however, as I don't really see why trichromatism is a disadvantage in low light conditions; surely low light sensitivity is more dependent on rods and eye structure?
An analysis of the wavelengths of the opsin pigments would be interesting. I must also remember to post another BIOL1040 response on eye structure and detection pigments (e.g. opsin) in cubozoans (i.e. box jellyfish) compared with other lineages (e.g. vertebrates).
Other interesting visual patterns include lungfish, which see four wavelengths, bees, which see UV, green and blue, and many bird species in which juvenile members see four wavelengths but adults only see three or two.
Then there are crustaceans....
Also, an interesting thing I read in a Scientific American concerned the human brain's way of interpreting colours. Apparently, we see in a blue-yellow channel and a green-red channel, preculding the existence of greeny-reds and bluey-yellows. Unless you torture a subject's poor brain for some time. I may have to search for the issue, I read it in a doctor's surgery some time ago....
Gravity Tropism
Hello (yet again),
Today in BIOL1040, I came across an interesting problem: how do plants sense gravity and grow in response (separately from other stimuli, such as when a seed is deeply buried)? It seems very unlikely that plants have 'gravity' eyes, so my suggestion is that some mechanism can detect which direction requires the most energy to grow in. Another hypothesis is that the mechanism which facilitates growth orients itself via gravity and is then constrained to provide growth in the upwards direction by structure. These mechanisms might be proteins or hormones stimulate such growth. Plant cells can also restrict their growth to upwards or downwards based on the orientation of their cellulose microfibrils, and since turgor pressure drives this kind of elongation, perhaps the direction of growth is easier to achieve once the first cells are aligned.
Josh H
Today in BIOL1040, I came across an interesting problem: how do plants sense gravity and grow in response (separately from other stimuli, such as when a seed is deeply buried)? It seems very unlikely that plants have 'gravity' eyes, so my suggestion is that some mechanism can detect which direction requires the most energy to grow in. Another hypothesis is that the mechanism which facilitates growth orients itself via gravity and is then constrained to provide growth in the upwards direction by structure. These mechanisms might be proteins or hormones stimulate such growth. Plant cells can also restrict their growth to upwards or downwards based on the orientation of their cellulose microfibrils, and since turgor pressure drives this kind of elongation, perhaps the direction of growth is easier to achieve once the first cells are aligned.
Josh H
Light Torture
Hello (again),
A conversation with Devin the Canadian laser physicist this afternoon revealed an interesting phenomenon: while infrared lasers cause 'heat' burns to skin, UV lasers cause 'sun' burns to skin and green lasers vaporise cardboard, apparently 400 nm (violet) lasers stimulate one's nerve endings, causing pain (much like a green-ant bite) but no damage to cells. I thought that this was a very interesting phenomenon and I didn't immediately see any direct cause. It seems unlikely that human nerve endings have channel rhodopsins (otherwise we would feel sensations depending on the lighting we are in! Perhaps good for parties...), so is the light directly affecting cells? Perhaps there is a protein that is directly affected by violet light, and the high intensities of lasers in the laboratory are high enough to cause an effect (this may be why the average party elicits no stinging sensations)?
Perhaps those of use with access to laser laboratories could investigate this phenomenon first hand (James...)? I think it would be worth the sting (which doesn't appear to have long term effects, other than those normally experienced by physicists) to be able to say, "I was stung by light!"
Josh H
PS: This would also offer a way to 'humanely' torture victims without causing any physical damage (and so leaving no hard evidence). This would mean that the phenomenon is well known and that it is currently in use....
A conversation with Devin the Canadian laser physicist this afternoon revealed an interesting phenomenon: while infrared lasers cause 'heat' burns to skin, UV lasers cause 'sun' burns to skin and green lasers vaporise cardboard, apparently 400 nm (violet) lasers stimulate one's nerve endings, causing pain (much like a green-ant bite) but no damage to cells. I thought that this was a very interesting phenomenon and I didn't immediately see any direct cause. It seems unlikely that human nerve endings have channel rhodopsins (otherwise we would feel sensations depending on the lighting we are in! Perhaps good for parties...), so is the light directly affecting cells? Perhaps there is a protein that is directly affected by violet light, and the high intensities of lasers in the laboratory are high enough to cause an effect (this may be why the average party elicits no stinging sensations)?
Perhaps those of use with access to laser laboratories could investigate this phenomenon first hand (James...)? I think it would be worth the sting (which doesn't appear to have long term effects, other than those normally experienced by physicists) to be able to say, "I was stung by light!"
Josh H
PS: This would also offer a way to 'humanely' torture victims without causing any physical damage (and so leaving no hard evidence). This would mean that the phenomenon is well known and that it is currently in use....
Electroreception (Wayne's 6th Sense)
Hello everyone,
Wayne has beaten me at posting about electroreception, but since my group's chosen BIOL1040 eConference assignment topic was electroreception differences between the Guiana dolphin and the Atlantic stingray, I thought I could provide some interesting information.
Wayne correctly summarises the origin of electroreception in fish: the lateral line. While I'm not sure what the lateral line has diversified into in the mammalian vertebrate lineage, the electroreception of monotremes and the Guiana dolphin arises from mechanosensory organs (and, interestingly, a different set of nerves). These same mechanosensory organs (whiskers, to us mortals) are widely used in marine mammal architectures (e.g. seals). The paper on the Guiana dolphin even suggested that the mechanosensory organs of other mammals may have branched into electroreceptive roles in other mammals, too.
Electroreception is quite an interesting phenomenon in itself: as far as I can tell, electroreception in mammals occurs directly via potentials across the nerve cells of the electroreception organs, usually with the assistance of a gel-like substance. Platypodes even have structural mechanisms that are thought to reduce noise ('daisy chains'). Fishies have far more structurally complex organs, but I'm not sure exactly how their sense works: it appears to be caused by a cell membrane potential gradient (as in mammals) but there are still 'kinocillia' in some electrosensory organs—perhaps movement of a kinocillium assists in detection?
Another interesting point is the fact that humans don't have mechanosensory whiskers. Is this because the nerve-blood vessel assemblies do not exist in humans, or do our lips (and 'fake' whiskers) occupy the same region? I have often heard that the lips are very sensitive to both pressure and temperature gradients. Would it be possible to biologically engineer electrosenses in humans? This brings up yet another interesting genetic biology question: how did electroreceptors evolve from mechanoreceptors? Did the nerve endings just become more exposed, until they could detect electric fields readily? This suggests that other animals could very easily have (limited) electroreceptive abilities, at least in water. Perhaps our lips can detect large electric field gradients, also?
I shall have to provide the paper references later, when I have more time. A search for 'Guiana dolphin electroreception' should reveal the paper on the Guiana dolphin, and a search for 'Euryhaline stingray electroreception) should reveal the Atlantic stingray paper. The stingray paper also considered the mechanisms of sensing, particularly whether or not the rays detect absolute field strength or field gradients: their findings suggest field gradients.
Josh H
PS: I have now received everyone's assignments, they are now awaiting marking (like good little assignments). Thank you.
Wayne has beaten me at posting about electroreception, but since my group's chosen BIOL1040 eConference assignment topic was electroreception differences between the Guiana dolphin and the Atlantic stingray, I thought I could provide some interesting information.
Wayne correctly summarises the origin of electroreception in fish: the lateral line. While I'm not sure what the lateral line has diversified into in the mammalian vertebrate lineage, the electroreception of monotremes and the Guiana dolphin arises from mechanosensory organs (and, interestingly, a different set of nerves). These same mechanosensory organs (whiskers, to us mortals) are widely used in marine mammal architectures (e.g. seals). The paper on the Guiana dolphin even suggested that the mechanosensory organs of other mammals may have branched into electroreceptive roles in other mammals, too.
Electroreception is quite an interesting phenomenon in itself: as far as I can tell, electroreception in mammals occurs directly via potentials across the nerve cells of the electroreception organs, usually with the assistance of a gel-like substance. Platypodes even have structural mechanisms that are thought to reduce noise ('daisy chains'). Fishies have far more structurally complex organs, but I'm not sure exactly how their sense works: it appears to be caused by a cell membrane potential gradient (as in mammals) but there are still 'kinocillia' in some electrosensory organs—perhaps movement of a kinocillium assists in detection?
Another interesting point is the fact that humans don't have mechanosensory whiskers. Is this because the nerve-blood vessel assemblies do not exist in humans, or do our lips (and 'fake' whiskers) occupy the same region? I have often heard that the lips are very sensitive to both pressure and temperature gradients. Would it be possible to biologically engineer electrosenses in humans? This brings up yet another interesting genetic biology question: how did electroreceptors evolve from mechanoreceptors? Did the nerve endings just become more exposed, until they could detect electric fields readily? This suggests that other animals could very easily have (limited) electroreceptive abilities, at least in water. Perhaps our lips can detect large electric field gradients, also?
I shall have to provide the paper references later, when I have more time. A search for 'Guiana dolphin electroreception' should reveal the paper on the Guiana dolphin, and a search for 'Euryhaline stingray electroreception) should reveal the Atlantic stingray paper. The stingray paper also considered the mechanisms of sensing, particularly whether or not the rays detect absolute field strength or field gradients: their findings suggest field gradients.
Josh H
PS: I have now received everyone's assignments, they are now awaiting marking (like good little assignments). Thank you.
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