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New Developments in Biology.

 
  

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Evil Scientist
11:41 / 28.07.06
As a result of a bit of chatter in the Lab Meta Thread I have decided to launch what is intended to be one of several general threads which will act as focal points for people to post information about any new developments they may discover in the various and myriad fields of science.

The hope being that these threads can collect together information regarding discoveries in relatively specific fields in order that we don't have to spend time data-mining which we could be using to discuss stuff. The further hope being that these general threads will act as launching points for more specific threads.

My only suggestion would be that people don't just dump a link down and leave it. Tell us why you found this development interesting, perhaps speculate on how this development or new knowledge can be utilised, ask questions about the bits that you don't quite get.

This first one is intended to focus on new discoveries in the general fields of biology and medical research. There is, I feel, plenty of scope there for us to play with.

So, to start.


Here is something that I read on the New Scientist website earlier today:

Each of your eyes transfers information to your brain at about the same speed as a fast Ethernet connection, US researchers have calculated.

I find the suggestion that our ability to transfer information via our optical nerve is limited by an evolutionary cost-benefit trade-off very interesting. If this is accurate then it seems we're pretty close to the upper limit of our optical information transfer without somehow improving the balance between cellular energy expenditure and speed of transfer.

How could this information be used to benefit us? I would speculate that, assuming further studies prove this to be accurate, that knowing the speed at which we can assimilate visual data could come in handy in the development and refinement of on-line/tv based teaching systems. Are there any neurologists in the house?
 
 
grant
14:34 / 28.07.06
knowing the speed at which we can assimilate visual data could come in handy in the development and refinement of on-line/tv based teaching systems

Funny, the first thing I pictured was a pilot at the controls of something like an SR-71 with no canopy windows, steering faster-than-vision with wires to the brain. I think I've read too much sci-fi, perhaps. But still, DARPA's big on how senses work.

Witness recent tongue research, for instance:

Researchers at the Florida Institute for Human and Machine Cognition developed a "Brain Port" that puts 144 electrods on the tongue. The pattern of electrode firing convey information such as sonar returns and compass headings. Michael Zinszer, a diver, described it as "Pop Rocks candies". The research team has built the system for sonar and compasses, and plans to integrate infrared sensors.

This is a logical next step, as the tongue has more nerve endings per inch than most other parts of the skin.


Viewing the human body as an information-processing machine, you know?
 
 
Proinsias
12:47 / 29.07.06
Perhaps not really brand spanking new in theory but certainly a huge leap now that it's getting properly tested and being put into practice.

Shocking developments in wound healing

If this technique is honed to a decent level could we be looking at a revolution in medicine?
I've been getting a bit carried away with the idea of this and perhaps it will develop a little slower than I would like. I want a wound healer attachment for my iPod and a regeneration booth in my dentist.

I didn't see any figures in the article relating to how much faster the wounds were healing, 10% faster or 200% faster? My science style web-fu is abysmal.
 
 
Dragon
00:37 / 30.07.06
A drug made to enhance memory appears to trigger a natural mechanism in the brain that fully reverses age-related memory loss, even after the drug itself has left the body, according to researchers at UC Irvine.

It looks like a new drug is just over the horizen for memory improvement. But, what I wondered was who would be benefiting from it -- that is, assuming it does materialize in the marketplace. Other factors may be cost, availability, and possible negative effects currently unforeseen.
 
 
Red Concrete
09:30 / 30.07.06
It looks like a new drug is just over the horizen for memory improvement. But, what I wondered was who would be benefiting from it -- that is, assuming it does materialize in the marketplace.

At a first guess, it could have applications in Alzheimer's Disease, maybe other dementias (of course proper clinical trials would be needed). If I remember correctly, the current treatments for AD can halt progression of the disease, but few reverse the dementia (or not very much).
 
 
*
21:01 / 10.08.06
Another one from the "Things That Make You Go 'Huh' Files."

Dogs have a form of sexually transmitted cancer which for the past 200 to 2,500 years has apparently spread via contagious tumor cells that escaped from their original body and now travel around the world as parasites.

Sounds like science fiction. If I didn't know Mr. Choi, I'd suspect him of being sensationalist.

Cancer researcher Robin Weiss at University College London and his colleagues analyzed genetic markers in recently collected and archived cancer cells from dogs in Italy, India, Kenya, Brazil, the United States, Turkey and Spain.

They found the tumor cells did not actually belong to the dogs they were in.

Rather, the cells were all genetically nearly identical, apparently stemming from a wolf or a closely related ancient dog breed from China or Siberia.
 
 
Dead Megatron
23:04 / 10.08.06
An airborne, self-sustaining undying, contagious malignant tumor? Cancer evolving into a separate living parasitical entity? That does sound like science fiction. Creepy.
 
 
*
23:29 / 10.08.06
It's not airborne. It is sexually transmitted.
 
 
Evil Scientist
06:50 / 11.08.06
Anyone can be John Sublime's dog, Gregory.
 
 
grant
14:30 / 11.08.06
Is this like an intermediary between cancer and virus? Viruses are *weird*.
 
 
Dead Megatron
19:42 / 11.08.06
It's not airborne. It is sexually transmitted.

re-reading the article, this time more slowly, I see I got it wrong. It was that part that confused me:

It is spread through sex and by licking, biting and sniffing cancerous areas

That is less creepy, but it's still creepy. And remember that 200 or 2000 years is very little time for evolution and mutation. Maybe in time, another few thousand years, we may have an air-borne self-aware all-contagious life-form evolved from a cencerous tumor that will destroy Earth's entire biosphere*.

*ok, I am only kidding by exageration, but that would make an interesting plot for a Doctor Who episode, at the very least...
 
 
grant
18:33 / 14.08.06
Ketamine is a fast-acting antidepressant, say NIMH researchers.

This sort of follows a general trend of psychedelic research recently.

Carlos Zarate, chief of the Mood and Anxiety Disorders Research Unit at the National Institute of Mental Health in Bethesda, Maryland, US and colleagues, set out to conduct a larger, more detailed trial of the drug’s antidepressant effects.

They analysed data from 17 participants, all whom suffered from moderate to severe depression and had failed to respond to at least two types of conventional drug treatments.

...Depression improved within one day for 12 of the 17 who received ketamine. These patients showed a 50% reduction in their symptoms, according to the Hamilton Depression Rating Scale.

...Overall, while nine of the 17 patients had a 50% reduction in their depression within the first 2 hours of ketamine treatment, only one person receiving the placebo experienced the same effect in this period of time.

The antidepressant effects of ketamine lasted for a week in four people and at least two weeks in another two subjects. "We didn't believe it would last that long," says Zarate.

Most anti-depressants work by boosting levels of the brain chemical serotonin. But ketamine acts in a different way, by reducing the effects of another neurotransmitter, called glutamate. This may explain the drug’s faster action, and suggest an alternative pathway for other antidepressant drugs, the researchers say.

...However, one of the reasons that clubbers abuse ketamine is for its hallucinogenic properties, such as seeing trails of light, and this was one of the most significant side effects occurring in the "vast majority" of participants, Zarate says.
 
 
astrojax69
23:21 / 02.10.06
well, it isn't really new developments, but it is pretty interesting biology from culture.

found this trawling about - fascinating about the strength capacity of the shrunken man! then there's more...

does this mess up the tin?
 
 
grant
13:28 / 20.10.06
One thing that all life forms on earth have in common is that they've been, one way or another, dependent on sunlight. Either they photosynthesize or they feed on creatures that photosynthesize (*). But no more. One mile below the surface of the earth, these gold mine microbes live on radiation.

(*)I'm not sure if this is true of the deep-sea volcanic vent critters, actually. Do the mineral nutrients they feed on come from detritus/sedimentary rocks, or not? Anyway, they don't FEED ON RADIATION so feh on them.
 
 
Evil Scientist
10:54 / 05.04.07
A big step forward in the development of vat-grown tissues and organs occurred recently with the successful production of human heart tissue from stem cell cultures.

A short feature from New Scientist:

Here.

A slightly longer one from The Guardian:

Here.

I think this is fantastic progress in a vital area of medical science. It's taken this group ten years of painstaking research to get this far, and may well take them another decade before they can construct an entire human heart. But what an achievement. Even as it stands now they will hopefully be able to use this technology to begin growing heart valves to help treat people with heart disease in the next few years (they're currently moving onto animal tests to investigate the viability of the tissue within a living system).

This particular paragraph caught my eye:

Prof Yacoub's inspiration has come not only from other scientists but also from an unexpected source - the celebrated British artist, Antony Gormley, who has donated a sculpture to the heart science centre. "We need a lot of experts from different fields but we also need a lot of imagination and a lot of understanding of how form interacts with function," said Prof Yacoub. "Art gives a lot of inspiration and beauty. And beauty is part of science."

That's how this kind of work gets done. By showing a little imagination and thinking (if you'll excuse the "business-ism) outside of the box.
 
 
grant
19:29 / 05.04.07
"...we also need a lot of imagination and a lot of understanding of how form interacts with function," said Prof Yacoub. "Art gives a lot of inspiration and beauty. And beauty is part of science."

Yes!
 
 
Rayvern
09:36 / 02.05.07
Probably old news to most of you guys, but I've just heard about it.

CPR Rethink

Thought it was a pretty important change ot the way we think about ER procedures.
 
 
Evil Scientist
10:24 / 02.05.07
Nice one dude. I've been on a defibrulator training course recently and they told me then that the system for doing CPR had changed to doing 30 compressions and then 2 breathes, and that if unable to give breathes just continue with compressions.

Nice to see what the biology is behind that.
 
 
grant
19:30 / 02.05.07
But did they give you syringes filled with frozen salt water?

That's when you *know* they're paying attention.
 
 
Evil Scientist
08:41 / 03.05.07
I'd assumed they were for when the zombies attack.
 
 
jentacular dreams
11:58 / 03.05.07
Very interesting. There's a lot of work being done on ischaemic preconditioning lately, where several small periods of oxygen depletion causes the body to produce a protective mechanism within cardiac myocytes, which can reduce the damage reperfusion does in case of a heart attack. The theory is that if this protective mechanism could be reproduced pharmacologically, an injection mid-attack could prevent damage upon recovery.

By extension such an injection might well work on more than just the mycocytes.
 
 
grant
16:02 / 03.05.07
What does that imply? More than just the myocytes... then... I don't follow.
 
 
grant
16:04 / 03.05.07
Are you talking about cryogenics?
 
 
jentacular dreams
16:59 / 03.05.07
Sorry I was reading and replying in a hurry. More that the (possible) drugs that could be used to treat heart cells during/following attacks (maybe adenosine for one) might also prove beneficial to the other cells of the body, which are probably undergoing similar stresses both during oxygen loss and reperfusion (especially nervous tissue).
 
 
Evil Scientist
11:06 / 09.05.07
An interesting suggestion for why the genes for cystic fibrosis are still with us in the New Scientist.

Here link here.

I wasn't aware that research had been done into it being linked with disease-resistance traits. But, assuming the data is actually correct (no actual physical evidence that possessing the gene for CF improves resistance to tuberculosis yet), we could be looking at a situation similar to that seen in Sickle Cell Anaemia whereby having one copy of the gene leads to a resistance trait and two copies lead to the disease.

In related news there is currently work progressing into drugs which will switch off the genes that produce non-functional proteins in conditions such as CF.
 
 
jentacular dreams
12:36 / 09.05.07
The second link is interesting, antibiotics are used routinely in a lot of biological experiments to keep cells expressing transfected genes (usually in plasmids), but even with the resistance genes coded for in the plasmid it suggests that antibiotics may have more far reaching effects on the proteome than they are currently given credit for.

With regard to the muscular dystrophy, upregulating utrophin (an embyronic analogue of dystrophin, the protein affected in DMD) levels seems to show a lot of promise. There's a minimal-kurdmenistani article here, or there's this) more recent review for those more versed in terminology. The first is reasonably low on biobabble, the second opens up at the utrophin section.
 
 
Closed for Business Time
12:36 / 07.06.07
Great story about a new way to create embryonic cells from skin cells in the NYT.

In a surprising advance that could sidestep the ethical debates surrounding stem cell biology, researchers have come much closer to a major goal of regenerative medicine, the conversion of a patient’s cells into specialized tissues that might replace those lost to disease.

The advance is an easy-to-use technique for reprogramming a skin cell of a mouse back to the embryonic state. Embryonic cells can be induced in the laboratory to develop into many of the body’s major tissues.
[...]
The new technique, developed by Shinya Yamanaka of Kyoto University, depends on inserting just four genes into a skin cell. These accomplish the same reprogramming task as the egg does, or at least one that seems very similar.
 
 
Evil Scientist
12:43 / 07.06.07
Some great news there. Although no timetable can be established yet for replication of the technique using humans. There are a few hurdles to get over first:

An immediate issue is whether the technique can be reinvented for human cells. One problem is that the mice have to be interbred, which cannot be done with people. Another is that the cells must be infected with the gene-carrying virus, which is not ideal for cells to be used in therapy. A third issue is that two of the genes in the recipe can cause cancer. Indeed 20 percent of Dr. Yamanaka’s mice died of the disease. Nonetheless, several biologists expressed confidence that all these difficulties would be sidestepped somehow.

“The technical problems seem approachable — I don’t see anyone running into a brick wall,” said Owen Witte, a stem cell biologist at U.C.L.A. Dr. Jaenisch, in a Webcast about the research, predicted that the problems of adapting the technique to human cells would be solvable but he did not know when.


Nothing too difficult though, relatively speaking.
 
 
Closed for Business Time
12:57 / 07.06.07
Indeed it's great news, and when (not IF) it can be used on human cells, well that's something to pop a bottle of Moet for IMO. However, this reminded of something - an essay I saw by Freeman Dyson. I'll post it here since it pertains to the post I made above, but I'm sure we could move discussion to the Transhumanism thread.

The games kids play...
Freeman Dyson


If home biotechnology becomes the latest fad, we'd
best start laying down rules, says Freeman Dyson

Fifty years ago at Princeton, I watched the mathematician John von Neumann design and build the first electronic computer to operate with coded instructions.

He knew that his invention would change the world, that the descendants of his machine would come to dominate the operations of science, business and government.

But he imagined that computers would always remain large and expensive. He failed to foresee computers becoming small enough and cheap enough to be used by kids to do homework. He failed to foresee the final domestication of computers as toys for three-year-olds.

There is a close analogy between Von Neumann's vision of computers as large centralised facilities and today's public perception of genetic engineering as an activity of large pharmaceutical and agribusiness corporations such as Monsanto.

I see a bright future for the biotechnical industry when it follows the path of the computer industry, the path that Von Neumann failed to foresee, becoming small and domesticated rather than big and centralised.

I recently spent a happy day at the Philadelphia Flower Show, the biggest flower show in the world, where breeders show off the results of their efforts. I was imagining what will happen when the tools of genetic engineering become accessible to these people.

There will be do-it-yourself kits for gardeners to create new varieties of roses and orchids. The technology will allow lovers of pigeons, parrots, lizards and snakes to breed new varieties.

Genetic engineering, once it gets into the hands of housewives and children, will give us an explosion of diversity of creatures, rather than the monoculture crops that big corporations prefer. New species will proliferate to replace those that farming and industrial development have destroyed.

Designing genomes will be a personal thing, an art form as creative as painting or sculpture. Few of the new creations will be masterpieces, but all will bring joy to their creators and variety to our fauna and flora.

The final step in the domestication of biotechnology will be biotech games, designed like computer games for children down to kindergarten age. But they will involve real eggs and seeds rather than images on a screen.

Playing such games, kids will acquire an intimate feeling for the organisms that they are growing. The winner could be the kid whose seed grows the prickliest cactus, or whose egg hatches the cutest dinosaur.

These games will be messy and possibly dangerous. Rules and regulations will be needed to make sure that our kids do not endanger themselves and others.

If domestication of biotechnology is the future, five important questions need to be answered:


Can it be stopped?

Ought it to be stopped?

If stopping it is either impossible or undesirable, what are the appropriate limits that our society must impose on it?

How should the limits be decided?

How should the limits be enforced, nationally and internationally?
Within a few decades, biotechnology is likely to replace most of our existing chemical industries and a large part of our mining and manufacturing industries.
Biotechnology will use land and sunlight as its primary sources of raw materials and energy. Fortunately, sunlight is most abundant in tropical countries where most of the world's people live and poverty is most acute.

Since land and sunlight are distributed more equitably than coal and oil, biotechnology can be a great equaliser, helping to narrow the gap between rich and poor countries.

With the aid of biotechnology, the children in every village of Africa could enjoy their fair share of the blessings of civilisation. They might even get to play the same biotech games.
 
 
grant
14:58 / 07.06.07
With the aid of biotechnology, the children in every village of Africa could enjoy their fair share of the blessings of civilisation. They might even get to play the same biotech games.

What does that mean?
 
 
Closed for Business Time
15:15 / 07.06.07
No idea. Anyone else?
 
 
grant
20:26 / 07.06.07
Genetic engineering, once it gets into the hands of housewives and children, will give us an explosion of diversity of creatures, rather than the monoculture crops that big corporations prefer. New species will proliferate to replace those that farming and industrial development have destroyed.


This bit also interests me, in that most "weight" that I've seen lately has been put behind the cultivation of heirloom breeds - the rare chickens mentioned in the "Chickens!" thread in Convo, heirloom tomatoes from our local CSA (and, maybe, my backyard), they're all things that used to be around a lot but didn't fit in with monoculture & industrial development. The tomatoes are irregularly shaped and bruise easily; the chickens are often dual-purpose or have unusual, showy plumage.

So it's interesting to me that Dyson's looking at novelty where I'm seeing a step back. I think he might be onto something, though.
 
 
Red Concrete
22:50 / 12.06.07
This could equally go into the new Environmental thread, but I reckon it's speculative enough that it probably shouldn't. A report (open access) suggests that melanin can use radiation to reduce NADH. Melanin's a pigment that's almost ubiquitous in nature, including in humans. This research shows that fungi which were grown in a way to increase their melanin content showed enhanced metabolic activity in the presence of ionising radiation. The implication being that such organisms could in theory live off radiation such as you might get from nuclear waste, analogously to the way that plants use the chlorophyll pigment to live off electromagnetic radiation.

This shouldn't be touted as a solution to nuclear waste, as that would probably be analogous to claiming that chlorophyll absorbing infrared is a solution to global warming... but it's a fascinating discovery. One suggested use for these fungi is as a food source for astronauts on long-haul space journeys, where there's plenty of cosmic radiation, but not much in the way of natural electromagnetic radiation.
 
 
Closed for Business Time
10:17 / 15.06.07
Plants recognise their siblings (pdf). And quoting from here:

Researchers at McMaster University have found that plants get fiercely competitive when forced to share their pot with strangers of the same species, but they’re accommodating when potted with their siblings.

“The ability to recognize and favour kin is common in animals, but this is the first time it has been shown in plants” Susan Dudley, associate professor of biology at McMaster University in Hamilton, Canada, said. “When plants share their pots, they get competitive and start growing more roots, which allows them to grab water and mineral nutrients before their neighbours get them. It appears, though, that they only do this when sharing a pot with unrelated plants; when they share a pot with family they don’t increase their root growth. Because differences between groups of strangers and groups of siblings only occurred when they shared a pot, the root interactions may provide a cue for kin recognition.”

Though they lack cognition and memory, the study shows plants are capable of complex social behaviours such as altruism towards relatives, says Dudley.


Huh? I'm... kinda stumped. Will this impact on anyone's ethical motives for being a vegetarian or vegan? I'm not sure that this shows that plants can suffer, and so would be included in a sorta Ryderian panoply of painist species, but I could be wrong - as the psychological and physiological attempts at defining emotion has yet to solidify into a coherent trajectory. This quote from Marian Dawkins, a zoologist at Oxford, illuminate what I'm trying to get at:

There are basically two approaches that have been adopted to studying animal emotions—the functional and the mechanistic. The functional approach means examining the role of emotions in human behaviour and then asking whether the function is the same in humans and non-humans. In many cases it is possible to apply Darwinian ideas to emotions and ask how emotions (in us an in other species) contribute to an organism's fitness. Fear, for example, is adaptive and functions to increase fitness both through motivating an animal to remove itself from danger and also to avoid similar situations in the future.

A widely used framework for viewing emotions in a functional context is that described by Oatley and Jenkins (1998) who see emotions as having three stages: (i) appraisal in which there is a conscious or unconscious evaluation of an event as relevant to a particular goal. An emotion is positive when that goal is advanced and negative when it is impeded (ii) action readiness where the emotion gives priority to one or a few kinds of action and may give urgency to one so that it can interrupt or compete with others and (iii) physiological changes, facial expression and then behavioural action. The trouble with this formulation is that it is so general and unspecific that it encompasses almost all behaviour in the sense that almost everything that humans or other animals do would have to involve such stages. Building a robot to behave in an autonomous and useful way, would almost certainly involve ensuring that it could evaluate its environment as either beneficial or harmful, give priority to one action that would be beneficial and then carry out the action. Worse, it even seems to apply to plants operating without nervous systems and using the simplest of mechanisms. For example, the parasitic plant, Dodder (Cuscata europaea) appears to “choose” which host plants to parasitize on the basis of an initial evaluation of a potential host's nutritional status. Kelly (1992) tied pieces of Dodder stem onto Hawthorn bushes which had been either fed extra nutrients or starved of nutrients. The transplanted growing shoots were more likely to coil on (“accept”) host plants of high nutritional status and grow away from (“reject”) hosts of poor quality and this acceptance or rejection occurred before any food had been taken from the host. It was thus based on an as yet unknown evaluation by the parasite of the host's potential food value and, within three hours, the growing tips could be seen either growing at right angles away from a rejected stem or coiling around one it would eventually feed from. By changing the time scale (hours rather than minutes) and the mechanism (growth rather than behaviour), we have an organism that shows appraisal, action readiness and action—the supposed functions of emotion without needing a nervous system at all. This suggests that merely defining emotions in a rather vague functional way of what they do in us and then asking whether there is evidence of similar functions in non-human animals is not going to be very fruitful. We need to look in more detail at how the functions are carried out.


The whole paper can be found here. (May be for subscribers only.)
 
 
Dead Megatron
18:59 / 03.07.07
Some interesting news in AIDS research that I thought you might want to know about:

cientists have constructed a custom enzyme that reverses the process by which the human immunodeficiency virus (HIV) inserts its genetic material into host DNA, suggesting that treatment with similar enzymes could potentially rid infected cells of the virus. In tests on cultured human tissue, the mutated enzyme, Tre recombinase, snipped HIV DNA out of chromosomes. Curing real infections by this or any other technique, however, would require mastering one of HIV's sneakiest tricks—its ability to hide from the immune system by laying dormant for months or years in host cells. HIV infects the immune system's disease-killing T cells by converting its genome into double stranded DNA and using the enzyme integrase to insert that DNA into a T cell's genome. Researchers have speculated that they could reverse this process with bacterial DNA-cutting enzymes they have adapted for adding and subtracting genes from mice and other multicelled organisms. To take that step, researchers from the Max Planck Institute for Molecular Cell Biology and Genetics and the University of Hamburg's Heinrich Pette Institute for Experimental Virology and Immunology began with the bacterial enzyme Cre recombinase, which exchanges any two pieces of DNA flanked on either end by a certain pattern of nucleotides (DNA subunits) known as loxP. HIV does not naturally contain loxP sites, so the team created a hybrid of the two DNA molecules, which they used to select a series of mutated Cre enzymes that were increasingly able to recognize the combined DNA. The final enzyme, Tre, removed all traces of HIV from cultured human cervical cells after about three months, the researchers report online today in Science. "This is the first demonstration of actual removal of the integrated virus from cells," says Alan Engelman, a molecular virologist at the Dana-Farber Cancer Institute in Boston. The results are promising, he says, but researchers have to make sure the slow-acting Tre enzyme works on real-world strains of HIV and figure out how to safely and precisely administer it in gene form to give it time to snip. Ideally, Engelman wrote in an editorial accompanying the new report, researchers would like to find a way to send Tre enzymes into the small number of T cells that carry the virus without producing new viral particles, which allows HIV to hide from both antiviral drugs and the immune system.

And here's the link for you to check for yourself
 
  

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