Tuesday, October 30, 2007

Long time no see

It certainly has been a long time. Last Saturday I went to the 40 year reunion of my year from Ryde High School. It was held 40 years since we stated our Higher School Certificate exams. About 25 or more years ago there was a reunion for the whole school. This reunion has been several months in the organizing. The organizers were able to contact somewhat over half of the individuals on the class list that they were able to get hold of. I was able to provide several leads to help them find some class members that I had ran into over the years.

There were a few classmates that I had been in occasional contact with after I finished Uni but that gradually dwindled over the years. It gradually dwindled down to one and even then I was in more regular contact with her brother who had been in another year at school. Still I bumped into classmates now and then. Usually they recognized me rather than the other way around. The last time was at a food market in Sydney about a year or so ago.

So it was good to see some old faces. Some I recognized easily, some I had to be told. Even in the latter cases it wasn't hard to see the face you knew from school in the face in front of you.

Of course there was the finding what we had been doing since school. Mostly what you could picture them doing, but there were some surprises. The group has been scattered over much of the country and in a few cases overseas. Still more were still in the Sydney district than anywhere else. Some including me came from interstate for the reunion.

One thing I will have got out of this is where those classmates are who are up here in Brisbane. And also where the ones in Canberra and Sydney are. A fair few are now in country locations.

One of the things that happens at events like this is finding out the background behind what happened back then. Why certain people behaved in certain ways. Who had a crush on whom and was too shy to show it back then.

The reunion was held in a large pavilion at Bobbin Head in Kuring Gai Chase National Park a bit North of Sydney. A picnic area with a good view right next to Cowan Creek, an off shoot of Broken Bay. Generally, had a great time.

Tuesday, September 25, 2007

A part of the solution

No single thing that we have done has led to our climate change problems. No single thing that we can do will solve them.

One thing that we have to do is use our energy resources more economically. Another is to find energy sources that do not put CO2 into the atmosphere and to reduce the amount of CO2 emitted by other sources. We have two main energy requirements, power for electricity and heat, and fuel or power to run vehicles.

We can supply electricity from sources that put no CO2 into the atmosphere. Nuclear, solar, wind , geothermal and hydroelectric are examples of such energy sources.

But we still need energy for vehicles. Internal combustion engines burning hydrocarbon fuels are a lightweight very flexible means of powering vehicles. But so long as we use petrochemicals , natural gas or the like they are a major part of the problem. There are difficulties using electricity in many vehicles. Overall it would be easiest if we could find alternative fuels.

One suggestion is hydrogen. This can be obtained by using electricity and the electricity can come from non CO2 emitting sources. Still hydrogen has problems with storage and with the embrittlement of metals that it can cause. It would be good if we could find a fuel source that removes as much greenhouse gases from the atmosphere as it adds.

This leads to biofuels. The idea is either to raise a crop that we can convert into fuel or to turn organic waste into fuel. The latter can only provide a small part of our energy need but every bit helps. The first can prove a lot more but there is a catch. Tho provide ethanol from corn or sugar cane or oils from soy beans etc. requires the use of a lot of agricultural land. It requires so much that it could seriously effect food production and with many crops we just don't have enough suitable land.

We need a better alternative and there is one. Grow algae in shallow ponds or plastic bags. It requires more than an order of magnitude less land than other crops used as fuel sources.

I was at a talk on research being done on producing algal biomass as a source of fuel. They are getting near. It is not yet economically viable but with current petroleum prices we are not far off. Work is being done to increase photosynthetic efficiency. An interesting possibility is the direct production of hydrogen by algae. This can occur under anaerobic conditions. Another possibility is that processing of the algal biomass can leave elemental carbon behind. This can be ploughed back into the soil in a very effective form of carbon sequestration.

And of course with such a source of fuel we can reduce our reliance on the Middle East. To the benefit of most of the world.

This of course is not the whole solution to our problems but I think it will be a big part of it.

Monday, August 13, 2007

So that's where the difference is

I was at a very interesting seminar and an interesting conversation afterwards.

When the Human Genome Project was completed everyone was surprised at how few gene there were. Only about 20-25,000 protein coding genes. It was not that much larger than that for much simpler organisms. So where was the greater complexity of humans and other mammals coming from? Where was the coding for the difference between human brains and those of other mammals?

People speculated that more complex organisms had much more complex regulatory systems in their genomes. Also splicing of different transcribed nucleic acid sequences together allows for an expanded proteome (suite of available proteins) from a genome that has not increased in size. The speculation is tha evolution mostly acts by affecting non-coding rather than coding DNA.

Now part of the regulatory apparatus is what are call micro-RNAs. These are short RNA sequences about 20-23 base pairs long. It was thought that there were several hundred and then thought that there were several thousand micro-RNAs in the cells of a given mammalian species.

The talk I went to today was on estimating how many micro-RNAs there were in a given species. It turned out to be a lot. An awful lot. In a mouse they estimated that there were over a million micro-RNAs. Less complicated organisms had an order of magnitude or more less micro-RNAs. And what was really interesting was that humans had over three million different micro-RNAs. Nothing else came close.

Guess what they think most of the extra micro-RNAs in humans are doing? That's right. They are probably a major part of the plan of the brain.

We have known the genetic alphabet for about fifty years. This is finding that there was a whole chunk of the dictionary that was much bigger and more important than we thought it was.

Tuesday, June 26, 2007

I didn't know it looked like that

This week the Institute for Molecular Bioscience holds its annual Winter School in Mathematical and Computational Biology. One of the talks was on the Visible Cell project. The aim of this project is to create three dimensional computer graphics models of mammalian cells for use by molecular biologists.

The cell type they have been looking at is the beta cell in the Islets of Langherans in the pancreas. What they have been doing is slicing cells into a lot of fine sections and taking electon microscope pictures of the sections and doing so at various angles. They are then using smoothers to join these sections together in the computer to create models of the cell.

Very impressive! And a lot of the organelles do not look like they to in textbook pictures. These pictures are usually based on single cross sections and can give quite misleading impressions of the three dimensional structures.

The mitochondria are not the little elliptical bodies you thought they were. They are long branching snake-like things. The Golgi apparatus does not look like a stack of pancakes. It is this elegant sparse lacy skeletal structure. The endoplasmic reticulum is similar. The cell is much more crowded than most illustrations would make you think it was.

In most of these cases my reactions were "I should have realized it wouldn't look like the pictures." and "Wow! Neat!"

Friday, April 13, 2007

The nervous system we didn't know we had

Most people have heard the claim that we only use 10% of our brain. Not many know the origin of this story. It appears to be a garbled version of the fact than only about 10% of the brain's cells are neurons.

Neurons are what we usually think of when we talk about nerve cells. They have long processes called axons and dendrites which nerve impulses travel along. These impulses are waves of electrical discharges. There are gaps between neurons called synapses. Chemicals called neurotransmitters diffuse across these gaps allowing one neuron to activate the next one thus allowing a nerve impulse to continue across the gaps between nerve cells. But a neuron may need a complicated combination of inputs before it will transmit an incoming signal.

The rest of the cells in the brain and in the rest of the nervous system are called glial cells. They have a similar origin to neurons but don't have the axons and dendrites. They act as a skeleton, they insulate neurons from one another and they provide oxygen and nutrients to the neurons. The nervous systems support system.

Or so it was thought. Now it looks as if there is less difference between the glial cells and neurons than we thought there was. While as far as we know glial cells cannot generate the action potentials, the nerve impulses many do have synapses and release neurotransmitters. They are also involved in preventing the build up of released neurotransmitters and regulating the activity .of synapses. They also are involved in controlling the development of the nervous system.

It looks as if glial cells, especially the astrocytes (the most common type in the central nervous system) provide much (most?) of the slow processing aspects of the brain. Things that happen in seconds rather than fractions of a second. As well as the fast processing system provided by the neurons we have a possibly larger slower system intertwined with it everywhere or almost everywhere. A nervous system we didn't know we had.

I recently went to a talk on some current work on this. A very important part for very many people. It looks as if many, probably most cases of chronic pain stem from feedback loops among astrocytes in the dorsal horn of the spinal cord. A caution, this is new work and much of this hypothesis is inspired by in vitro experiments on nerve cells. Much needs to be done to confirm this.

Chronic pain is pain which persists after the injury or disease which originally caused it is gone. It is when rather than being the symptom of a disease the pain is the disease.

Pain is transmitted to the brain by parts of the dorsal horn of the spinal cord. As I understand it if there are a lot of pain signals coming in it appears that the astrocytes in these regions can get trapped in a feedback loop stipulating each other by the released neurotransmitters glutamate and ATP, especially the latter. In this state they continually excite the pain transmitting neurons even after there are no more pain signals coming in from the body. It's like pushing a throttle forward and finding that it is jammed there and you can't turn the motor off.

If this is correct then there is hope for chronic pain sufferers. We need to find a way to reset the spinal cord. I don't know how and I don't know when we will be able to do this. Not for a while but we should be able to do it.

Tuesday, April 10, 2007

It's been too long

since my last blog post. For various reasons I haven't been able to settle down to write one.

But more important I'd been out of work for too long. At last I'm back at work, doing something I find interesting and getting enough money to have a reasonable set of choices of things to do outside of work.

The downside is that I had to move interstate to get this job. For now I'm living in pretty basic accommodation in a hostel mostly catering to overseas students. Ah well, it cuts costs. And I don't mind living in Brisbane.

I'm working as a research assistant for the University of Queensland in the Institute for Molecular Bioscience and the Department of Mathematics. I'm working on model-based clustering, in particular the use of finite mixture models for clustering.

You see ,clustering is answering the questions does this data fall into groups, if so how many and which observations are in which groups. The thing about cluster analysis is that you only have the observations, not the groups that they belong to. For any of them. You have to create the groups, not put the observations into known or predefined groups. That is classification.

Not surprisingly it is a less well defined problem than classification. Usually you create a matrix of distances between observations. (And one of your first decisions is how to define these distances.) Then you put the observations through some algorithm for joining them up into groups. A problem with this approach is that it is difficult to come up with an objective measure of how good the classification that you come up with is.

I'm working on testing improvements in one alternative approach. This is to assume that the results come from a mixture of distributions of specified but flexible forms. You put the observations into an initial clustering and then improve it by iterative methods. In principle this should put the clustering on a better mathematical foundation.

One of the nice things about the job is that I get to go to some very interesting seminars at the IMB. And since I started out in Biology I find some of them very interesting indeed.

Let's see there was the talk on larval development in sponges. Fascinating. The larvae are more structured than the adults. They are more closely related to the rest of the animals than we thought. You see at one time we thought Porifera (sponges) might have developed from protists independently of the rest of the animals.

But here you see a sponge larva. And it looks like nothing so much as a planula, the larval form of such things as hydras and jellyfish. With a couple of interesting differences. One is in the arrangement of the flagella. But the big one is that it is radially symmetrical where a planula is bilaterally symmetrical even though the adult Cnidaria (Hydras, jellyfish, corals, sea anemones etc.) are radially symmetrical. There are a couple of common factors producing developmental gradients both in Poriferan and Cnidarian larvae. The thing is in the Cnidaria one of them runs longitudinally and one runs dorso-ventrally. In the Porifera they both run longitudinally. This suggests some interesting questions about the development of radial and bilateral symmetry in animals.

Things are looking up. Finally!

Coming up soon, the nervous system we didn't know we had.

Friday, September 22, 2006

Bring me the head of ...

First off, profound apologies are due to the Minister for Foreign Affairs and Trade, Alexander Downer. He is not responsible for the horrendous mucking around and obstruction and sheer bastardy that Zoe Brain has had to endure from the Australian Passport Office. I'm glad I was wrong.

It appears that the main culprit is the Acting Director of the APO, Bob Nash. He is guilty of everything nasty that I suspected Downer of and worse. Some other high ups in the APO might be involved as well but I don't know yet. At most it looks like a few scumbags at the top. The case officer and the counter staff have all done the right thing in difficult circumstances.

Zoe has put up a summary of what has happened on her blog.

Briefly the Australian Passport Office has been looking for ways to prevent Zoe from obtaining an Australian Passport rather than looking for ways around unintended and unanticipated effects of regulations. The regulations were designed to handle more normal cases of transsexuality. Her case is unusual in two major ways.

One is the gender change was not being due to surgery. Although she is on hormone treatment now most of the changes have been spontaneous. This is an extremely rare condition. We can only guess about the cause. It's probably a rare combination of factors.

The other is her marriage surviving this ordeal. Marriage has several functions. Not everyone will place a high importance on all of them and a marriage can still be important and valuable if some of them are absent or handled another way.

One of its traditional functions was to provide a situation in which sexual activity was socially condoned. There have been religious prohibitions on sexual activity other than heterosexual activity within a marriage.

Another function is do act as a public affirmation of commitment by the partners. Another is to act a financial and social partnership.

And of course it is supposed to act as a framework for bringing up children.

One does not necessarily dissolve an existing marriage if the sexual side of it disappears but the other aspects are still functional. Especially if there are children involved.

Zoe and Carmel intend to stay together to raise Andrew. And while the sexual side of their relationship is now no longer functional the rest is. Their marriage still means something to them and they wish to preserve it despite the changes it has been through.

The legal situation is clear. The people contracting a marriage have to be of different genders at the time of the wedding. A subsequent change of gender is irrelevant

But there are people trying to make a point about their opposition to homosexual marriage. To make their point they are freaking out about any same sex marriage even such an unusual one as this. This appears to be what is behind the actions of the APO. We had the Acting Director of the APO saying “Under the Marriage Act, we can't have married people changing their gender”. What business is it of his? How dare he try to break up a marriage? His job is to administer the Passports Act. Not to use his office to enforce his idea of what marriage should be. He is supposed to help people get passports not look for ways to stop them from obtaining passports.

The APO have deliberately violated the intent of the Law and ended up violating its letter as well. They have asked for irrelevant and intrusive documentation on the pretext of proof of identity. When asked to give reasons for their action they missed the legally required deadline. Their reply was evasive and did not answer the questions. In short they have shown a complete lack of good faith.

Fortunately Zoe was able to work around them. The Department of Immigration and Multicultural Affairs was much more helpful. They were appalled by the APO's treatment of Zoe. They did the unusual step of issuing a visa on Zoe's UK Passport. In other words they exploited rarely used technicalities to help an Australian citizen.

Zoe should never have been put through this ordeal. The Head of the APO at least has shown his complete unfitness for his office. They must be prevented from doing this to anyone else. Their next victim might not survive.

I have written the following letter to the Foreign Minister.

The Hon Alexander MP
Minister for Foreign Affairs and Trade
Parliament House

Mr. Lloyd Kilworth Flack
18th September 2006

Re: Passport application by Zoe Ellen Brain and actions of the Australian Passport Office

Dear Mr Downer,

I am writing to complain about the reprehensible treatment of a friend of mine by certain staff members of the Australian Passport Office. Some staff members including the Acting Director Bob Nash are trying to make it difficult or impossible for her to obtain a usable Australian Passport.

They appear to be doing so because of bigotry against transsexuals. They have intentionally violated the spirit of the Law. In their presumption and arrogance they have carelessly ran the risk of violating the letter of the Law and have ended up doing so.

Alan Brain has been a friend for over thirty years. About sixteen months ago I heard from him that he was undergoing a spontaneous sex change. We can still only speculate about the cause. Whatever it was it is extremely rare. This aggravated a repressed sexual dysphoria. I knew Alan very well for a long time. If he claimed that there was a mismatch between the gender of his brain and that of his body then I have no doubt that the claim was correct. He was not the type of person that would imagine such a thing.

Alan is now Zoe and much more comfortable as a woman than she ever was as a man. From what I now know it is obvious that there always was a degree of intersex. She is now living as a woman and recognized as such by Medicare. Her Citizenship Certificate has been changed to reflect the reality of her current gender. She is now receiving hormone treatments to regularize her status and will require gender affirmation surgery for this purpose and to minimize the risk of cancer. Her appearance now is female and she would have difficulty passing as a male.

Her marriage has survived these events and she and her partner Carmel are determined to stay together to bring up their son Andrew now five years old.

To have this surgery she will have to travel overseas as the required surgery for her particular case is not available in Australia. She will also have to travel overseas for conferences related to the PhD that she is currently working towards. To do so she requires and is entitled to a usable Australian passport. That would be either a female passport or one with an indeterminate gender. Since a male passport would be at variance with her appearance it would be embarrassing, inconvenient and in some circumstances actually dangerous.

As an Australian citizen she is entitled to an Australian passport if the required forms are filled in, fees paid and proof of identity and citizenship given. There are exceptions related to crimes and security and so on but they do not apply in this case. As someone who has undergone a gender change other than as a result of an operation and whose marriage has survived this harrowing ordeal she does not fit into the normal categories that the regulations are based around.

In a case such as hers the Australian Passport Office should be seeking ways they can give her a passport without breaking the regulations rather than seeking reasons to deny her a passport. If they could not do so they should have referred the case to you so you could make a Ministerial Determination to cover these exceptional circumstances.

They have not done so. They have been deliberately obstructive.

Much more proof of identity and citizenship was given than your website asks for. There cannot be an reasonable actual doubt about her citizenship and identity. They have asked for things such as proof of surgery when the sex change was a result of a medical condition rather than surgery. They have sought private and superfluous medical information. This a gratuitous invasion of privacy.

The rejection was made by Policy Section and was done so immediately and continued despite all additional information that they were given. They claimed that she had not provided sufficient documentation to prove her identity and citizenship. This claim is preposterous since far more documentary evidence than is usually asked for was given.

A demand was made for the reasons for the decision. The Department was given 28 days to reply in writing as was required by law. They did not do so within the required time. The reply did not answer the questions asked and could only be regarded as an evasion. The excuse for the delay was the absence of necessary personnel. The deadline given made plenty of allowance for this possibility. When I consider the rest of the APO's actions the only conclusion that I can come to is that they deliberately tried to reply as close to the deadline as possible and unanticipated absences then led to them missing the deadline. In other words they deliberately violated the spirit of the Law and as a result violated its letter as well.

The Acting Director of the APO Bob Nash has claimed that in order to gain a female passport Zoe would have to divorce Carmel. According to written advice from the Attorney General, the Hon Phillip Ruddock a change of gender does not invalidate an existing marriage, that only the genders at the time of the marriage are relevant. Mr. Nash has ignored this advice, which was in his possession. Asking someone to divorce because it is administratively easier or because it fits in with one's ideology is an obscene and insolent act. It is gross abuse of power.

I do not know which other APO staff are behind this fiasco. It appears to be only a few individuals high up in the department. The case officer involved and the counter staff acted with courtesy, propriety, decency and efficiency in a difficult situation.

Mr. Downer I request that you promptly make a Ministerial Determination overriding Mr. Nash's decision and grant Zoe the Passport to which she is entitled as an Australian citizen. I request that an apology be issued and reasonable compensation for inconvenience and suffering be paid. I request that procedures be modified to reduce the risk of something like this happening in future. At present the Australian Passport Determination 2005 Explanatory Notes allow the APO to treat transsexuals as if they were criminals.

Further I request that Bob Nash be removed from his office and placed somewhere where he can do no further harm. And that the same be done to anyone else involved in deliberately making things difficult for Zoe. Usually I find stuff-ups more believable than malice. In this case only malice fits. (Rather like the Lebanese ambulance case. Normally I would prefer collateral damage as an explanation, but only a hoax fits.) Anyone with with an adequate supply of common decency would have tried to help, to find a way to give Zoe her passport. The opposite happened. Their job is to serve the Australian public, not to use their office to pursue private agendas and prejudices.

If they claim that they believed that what they were doing was right I will only be angered more. Self-righteousness is one of my pet hates. By self-righteousness I mean trying to feel or appear virtuous and avoiding looking at the cost to others of doing so. It adds insult to injury. In this case it appears to have a solid foundation of moral cowardice.

This is not a case of political correctness. This is a case of Right Wing Death Beasts seeking retribution for a wrong against one of their own. Deliver the heads on pikes or on platters, doesn't matter.

Yours Sincerely,
Lloyd Kilworth Flack MStats BSc

I urge others to write letters of complaint to the Minister. I want the culprits put where they can do no further harm. In a couple of places I suggested that they be sent to count parasites on penguins in Antarctica. If he receives enough complaints he might look at this seriously.