ALIFE-XII Proceedings

Are available as a 95MB pdf file. Sample chapters and the Table of Contents are also available.

Our own work, Using Meta-Genetic Algorithms to tune parameters of Genetic Algorithms to fi nd lowest energy Molecular Conformers by Brain and Addicoat Proc. of the Alife XII Conference 2010 pp 378-385 is available as an 11 Mb pdf.

Abstract
Determining the electronic structure of long chain molecules is essential to the understanding of many biological processes, notably those involving molecular receptors in cells. Finding minimum energy conformers and thus electronic structure of long-chain molecules by exhaustive search quickly becomes infeasible as the chain length increases. Typically, resources required are proportional to the number of possible conformers (shapes), which scales as O(3^L) where L is the length. An optimized genetic algorithm that can determine the minimum energy conformer of an arbitrary long-chain molecule in a feasible time is described, using the tool, PyEvolve. The method is to first solve a generic problem for a long chain by exhaustive search, then by using the pre-determined results in a look-up table, to make use of a Meta-GA to optimize parameters of a simple GA through an evolutionary process to solve that same problem. By comparing the results using the tuned parameters obtained by this method with the results from exhaustive search on several molecules of comparable chain length we have obtained quantitative measurements of an increase in speed by a factor of three over standard parameter settings, and a factor of ten over exhaustive search.

It's not written for a general audience, but parts may not be too heavy going for some of my readers.

Home Again, Home Again Jiggity Jig

Normal blogging will resume shortly, as soon as my body clock has reset. I'm getting too old for this kind of thing. Travel that used to be no problem when I was in my thirties is now rather more gruelling now I'm 52. Still, better start preparing for the next conference, in New Orleans in November.

ADVERT: A Gender Agenda - Help Wanted

Transgender and Intersex Project Officer

Part Time (approx 25 hours per week)

$40,000 - $45,000 (neg) with Option to Salary Package

A Gender Agenda is seeking a project officer to coordinate two exciting new projects which will run until Dec 2011. The position will be responsible for organising a range of community events and developing an information and referral resource.

Applicants will be required to demonstrate:

- an ability to work independently and to meet deadlines

- an ability to work effectively with a wide range of people

- strong oral and written communication skills

- basic computer literacy and administration skills

- strong knowledge of transgender and intersex issues (We will also consider applicants who have a demonstrated ability to work with marginalised communities if they are genuinely committed to learning more about these issues)

Applications close 3rd September 2010 and should briefly outline relevant skills/experience.

For more info contact community@genderrights.org.au or call Peter Hyndal on 0419 471 756.

Intersex and Trans* people are strongly encouraged to apply

There is something Rotten

In the state of Denmark. Fortunately though, I've changed my socks.

The workshops before the conference were interesting - my only complaint is that there wasn't more time available.

Anyway, it's now 6AM, and I'm raring to go after a minor pub crawl last night with some of the other attendees. At $10 a glass, I wasn't tempted to over-indulge. I did get to see a little of Odense, and more importantly, scored a Lego set that my son wanted.

Breakfast is at 0630, then the bus to the University leaves at 0745. I'll try to blog the conference using the University's WiFi - the conference organisers supplied us with guest logins.

Disordered or Just Different? Myth, Science, and Sexuality.

I've blogged about one of the true experts in the biology, and the science of sex and gender, Dr Veronica Drantz before.

This is a slideshow of her latest presentation on the subject. The content is similar to what is currently being taught to psychology and medical students at the ANU - though without the trenchant criticism of the Theologues and Quacksalvers.

Disordered or Just Different? Myth, Science, and Sexuality.

View more presentations from drdrantz.

I've scheduled posting this in advance, because I'll be on my way to Denmark when it gets published.

Lessons From Recent History

Throughout history, poverty is the normal condition of man. Advances which permit this norm to be exceeded — here and there, now and then — are the work of an extremely small minority, frequently despised, often condemned, and almost always opposed by all right-thinking people. Whenever this tiny minority is kept from ...creating, or (as sometimes happens) is driven out of a society, the people then slip back into abject poverty. This is known as "bad luck."
-- R.A.Heinlein



Take sex away from people. Make it forbidden, evil. Limit it to ritualistic breeding. Force it to back up into suppressed sadism. Then hand the people a scapegoat to hate. Let them kill a scapegoat occasionally for cathartic release. The mechanism is ages old. Tyrants used it centuries before the word "psychology" was ever invented. It works, too.
-- R.A. Heinlein

The Park in the picture retained its 1969 character until 1989, when the Soviets withdrew. By 2001, after just 10 years of feudal infighting and Theocratic rule, it was in the same state it is now.

The Fractal Futurama Evolution Episode

Link Here



For a view of a similar topic from 1983, have a look at the Prologue to James P. Hogan's Code of the Lifemaker.

And in about 48 hours time, I'll be on my way to ALIFE-XII - the 12th International Conference on the Synthesis and Simulation of Living Systems, where I'm giving a paper.



The paper is called "Using Meta-Genetic Algorithms to tune parameters of Genetic Algorithms to find lowest energy Molecular Conformers, by Brain and Addicoat.

We used evolution to evolve a good evolutionary algorithm for helping determine biological properties of long-chain molecules. The good algorithms got to survive and breed, the less fit ones died out, till we had a "tuned" genetic algorithm that worked well.

As above, so below - with variations on a theme.

Seen on a Forum

Let's put the seniors in jail and the criminals in a nursing home.

This way the seniors would have access to showers, hobbies and walks.

They'd receive unlimited free prescriptions, dental and medical treatment, wheel chairs etc and they'd receive money instead of paying it out......

They would have constant video monitoring, so they could be helped instantly, if they fell, or needed assistance.

Bedding would be washed twice a week, and all clothing would be ironed and returned to them.

A guard would check on them every 20 minutes and bring their meals and snacks to their cell.

They would have family visits in a suite built for that purpose.

They would have access to a library, weight room, spiritual counseling, pool and education.

Simple clothing, shoes, slippers, PJ's and legal aid would be free, on request.

Private, secure rooms for all, with an exercise outdoor yard, with gardens.

Each senior could have a PC a TV radio and daily phone calls.

There would be a board of directors to hear complaints, and the guards would have a code of conduct that would be strictly adhered to.
............................................................
The "criminals" would get cold food, be left all alone and unsupervised.
Lights off at 8pm, and showers once a week.
Live in a tiny room and pay £900.00 per month and have no hope of ever getting out.

Yvonne Elliman If I Can't Have You

If I lost just a little weight - that would be a good look on me... yes, I know, "Vanity, Thy Name is Woman" and all that. But I'm not just the cool objective scientist all the time.

Male Gender Identity in an Individual With Complete Androgen Insensitivity Syndrome | American Trans Man

Another Read The Whole Thing essay. This one from American Transman, detailing a case which until I read it, I thought was physically impossible.

Well Reality doesn't care what we think. It takes only one ugly little fact to slay the most elegant theory.

So please read Part 4 Male Gender Identity in an Individual With Complete Androgen Insensitivity Syndrome | American Trans Man for a really good analysis of a rare situation, and some postulated modifications to existing theory to account for it. A really good piece of work.

The Fireman's Wife

As a follow-up to a previous post, there's one of the best pieces of real journalism I've seen for quite some time. It's The Fireman's Wife in the Houston Press.

It's in-depth, well-researched, and objective. Moreover, it's complete, or as near as makes no odds. Unlike most of the pieces in the press that have masqueraded as news articles, it's not one-sided. It's not a mere parroting of transphobic smears. Neither does it attempt to gloss over details that either side would prefer to be hidden, such as the widow's chequered past, nor the gross misconduct by the opposing side's lawyers - misconduct that has brought them to the attention of the Texas bar.

I won't quote from it; it's lengthy, but it has to be to be complete, and it's not a story that can be easily summarised in sound-bytes. As they say, Read The Whole Thing.

Nerve Regeneration

Ok, so far it's only in mice. It's not ready for prime time. But it seems that just as we might be acquiring the ability to make an artificial shunt, a neural bypass around spinal chord injury, it may not be necessary. We may be able to get the body to do it for us. Avoiding a neoplasm in the process is going to be a neat trick though.

From the UC Irvine :

Researchers for the first time have induced robust regeneration of nerve connections that control voluntary movement after spinal cord injury, showing the potential for new therapeutic approaches to paralysis and other motor function impairments.

In a study on rodents, the UC Irvine, UC San Diego and Harvard University team achieved this breakthrough by turning back the developmental clock in a molecular pathway critical for the growth of corticospinal tract nerve connections.

They did this by deleting an enzyme called PTEN (a phosphatase and tensin homolog), which controls a molecular pathway called mTOR that is a key regulator of cell growth. PTEN activity is low early during development, allowing cell proliferation. PTEN then turns on when growth is completed, inhibiting mTOR and precluding any ability to regenerate.

The actual paper on the subject is PTEN deletion enhances the regenerative ability of adult corticospinal neurons by Liu et al, Nature Neuroscience (2010) doi:10.1038/nn.2603

Despite the essential role of the corticospinal tract (CST) in controlling voluntary movements, successful regeneration of large numbers of injured CST axons beyond a spinal cord lesion has never been achieved. We found that PTEN/mTOR are critical for controlling the regenerative capacity of mouse corticospinal neurons. After development, the regrowth potential of CST axons was lost and this was accompanied by a downregulation of mTOR activity in corticospinal neurons. Axonal injury further diminished neuronal mTOR activity in these neurons. Forced upregulation of mTOR activity in corticospinal neurons by conditional deletion of Pten, a negative regulator of mTOR, enhanced compensatory sprouting of uninjured CST axons and enabled successful regeneration of a cohort of injured CST axons past a spinal cord lesion. Furthermore, these regenerating CST axons possessed the ability to reform synapses in spinal segments distal to the injury. Thus, modulating neuronal intrinsic PTEN/mTOR activity represents a potential therapeutic strategy for promoting axon regeneration and functional repair after adult spinal cord injury.

As they say... more please, and faster.

Travel Issues

New Information The U.S. Transportation Security Administration (TSA) has advised all airlines that, effective November 1, 2010, all passenger reservations containing any U.S. city segment or flying over U.S. airspace must contain full Secure Flight Passenger Data (SFPD). Reservations without full SFPD will be rejected by the TSA, and airlines will be subject to penalties.
* Provide Secure Flight Passenger Data information: When making a travel reservation, travellers should provide the required data elements (full name, gender and date of birth).

I'm due to attend a conference in New Orleans in November.

I've asked the TSA which gender I should report - the one on my UK Birth Certificate, the one on my UK passport, the one on my Australian passport, or by one reading of Wilma Wood vs C.G studios, none of the above?

Meanwhile... I'm making contingency plans to fly to Mexico, then travel overland from there. Just in case.

This is silly. But then, that's nothing new in the collision between legalities and biological realities.

Oh Oh

Figures are for the USA

From the Australian Human Rights Commission

Dear all



Thank you very much for your contribution to the Commission’s brief consultation regarding the terminology used to describe people with a range of sex identities and gender identities.



The majority of responses we received supported some means of separating issues relating to sexual orientation from those relating to sex and/or gender identity and those relevant to people who are intersex.



There was no consensus regarding the term ‘intersex and sex and/or gender diversity’. There was also not majority support for the use of the term ‘sex and gender diversity’. A number of submissions supported retention of the overall phrase Lesbian, Gay, Bisexual, Trans and Intersex (LGBTI).

In response to the comments that we have received we have decided to proceed as follows:

1. We will create three distinct subsections within the one page on our website:

· Sexual orientation and human rights

· Sex and/or gender identity and human rights

· Intersex people and human rights.

2. Within each of these subsections we will acknowledge the diverse range of identities and the range of human rights issues of concern.
3. Due to its internationally accepted use, and due to the submissions that argued for its retention, we will retain the use of the phrase LGBTI, only as the entry point to this part of the Commission’s website. We will replace the term ‘transgender’ with the term ‘trans’. We will acknowledge the controversies regarding terminology at the top of this page.
4. We have raised the issues of concern about the use of the term ‘gender equality’ and ‘men’ and ‘women’ on the Commission’s website with the Sex Discrimination Commissioner who is currently considering these concerns.

Thank you again for your participation in this consultation.



The Commission is hoping to begin a small project regarding federal protection from discrimination on the grounds of sexual orientation, sex identity and gender identity (including people who are intersex) shortly. We will be in touch again about this work towards the end of August.



Kind regards
Kate Temby



Kate Temby
Acting Director
Human Rights Unit

Australian Human Rights Commission

Level 8 Piccadilly Tower, 133 Castlereagh St, Sydney NSW 2000
GPO Box 5218, Sydney NSW 2001
T +61 2 9284 9693 F +61 2 9284 9797 M 0410 645 113
E kate.temby@humanrights.gov.au W www.humanrights.gov.au

We're getting there.

My Life Recently

To Arms! Two Arms!

From Science Daily:

"We've developed the enabling technologies to create upper-extremity prosthetics that are more natural in appearance and use, a truly revolutionary advancement in prosthetics," said APL's Michael McLoughlin, the program manager. "Now, in Phase 3, we are ready to test it with humans to demonstrate that the system can be operated with a patient's thoughts and that it can provide that patient with sensory feedback, restoring the sensation of touch."

The team will develop implantable micro-arrays used to record brain signals and stimulate the brain. They will also conduct experiments and clinical trials to demonstrate the ability to use implantable neural interfaces safely and effectively to control a prosthesis, and optimize arm control and sensory feedback algorithms that enable dexterous manipulation through the use of a neuro-prosthetic limb.

"We will be working very closely with the University of Pittsburgh and the California Institute of Technology for their experience in brain computer interfaces, the University of Chicago for their expertise in sensory perception, the University of Utah for its capabilities in developing implantable devices suitable for interfacing with the human brain, and HDT Engineered Technologies for their skill in building prosthetic limb systems," McLoughlin said.

Both Pittsburgh and CalTech have conducted research using chips with hair-like electrodes to record neurological signatures in the brain. Last year, in an independent effort, Pittsburgh showed that a pair of macaque monkeys with tiny chips implanted in their brains could operate a robotic arm just by thinking about it. Wires carried the signals through the skull, and then computer software converted these signals into robotic arm movements.

Within the year, the APL-led team will initiate testing with a high spinal cord injury patient. "Initially, we have targeted the quadriplegic patient population because they have the most to gain," McLoughlin explained. "Unlike most amputee patients who have other options in terms of care and independence, these patients are totally dependent on others for most things. There is no alternative. Their lives will be truly transformed by this advancement."

As I said in 2007...

The difficult thing is going to be decoding the sensory data from parts of the body below the break. But simple control of a prosthetic, that is at worst only a decade away.

I expect this to be out of the Labs and into series production by about 2015.

Thought For Today

After playing with my son on his Wii, using a second controller:

Mike Oldfield - Ascension

The meek shall inherit the Earth - the rest of us, the Stars.

Equality?

From the UK Equality Act 2010 :

Equality Act 2010 (c. 15)
Schedule 3 — Services and public functions: exceptions
Part 7 — Separate and single services

Gender reassignment
28
(1) A person does not contravene section 29, so far as relating to gender reassignment discrimination, only because of anything done in relation to a matter within sub-paragraph (2) if the conduct in question is a proportionate means of achieving a legitimate aim.

(2) The matters are—
(a) the provision of separate services for persons of each sex;
(b) the provision of separate services differently for persons of each sex;
(c) the provision of a service only to persons of one sex.

Equality Act 2010 (c. 15)
Schedule 9 — Work: exceptions
Part 1 — Occupational requirements
(3) The references in sub-paragraph (1) to a requirement to have a protected
characteristic are to be read—
(a) in the case of gender reassignment, as references to a requirement not to be a transsexual person (and section 7(3) is accordingly to be ignored);

So what does that mean? It means that there is one "protected" class where protection is explicitly removed, not granted. It means that a gender recognition certificate is not worth the paper it's printed on. Rather than being a recognition that they are of the target gender, it's a nullity, as the law states that they're not, not really. This is made clear in the explanatory notes.:

Gender reassignment: paragraph 28

749. This paragraph replaces a similar provision in the Sex Discrimination Act
1975.
Example
A group counselling session is provided for female victims of sexual assault. The organisers do not allow transsexual people to attend as they judge that the clients who attend the group session are unlikely to do so if a male-to-female transsexual person was also there. This would be lawful.
...
Schedule 9: Work: exceptions
Part 1: Occupational requirements

A counsellor working with victims of rape might have to be a woman and not a transsexual person, even if she has a gender recognition certificate, in order to avoid causing them further distress.

The provisions of the Gender Recognition Act 2004 that over-rode that 1975 act have now been repealed. There is a distinction between "women" and "transsexual persons with (or without) gender recognition certificates" now.

Now of course, who could reasonably object to a councellor whose appearance might be upsetting to a rape survivor? In such cases, we cannot afford to be too precious about rights of employment, we must consider the victims first and foremost.

But it's not about appearance. It's not about the victims and their feelings. It's about transphobic prejudice. It's now legitimate to refuse help to victims who are "transsexual persons" because of the transphobia of others. There are other consequences too.

Good	Bad
Noted "Womyn born Womyn" Female At Birth founder of the New Radical Lesbian Feminist Front, dedicated to keeping Trans women out of women's space, including rape crisis centers. A "real" woman who it is illegal to discriminate against.	Not a woman, but a transsexual person. Someone who it is explicitly legal to discriminate against as their presence - either as councellor or as victim - may be too upsetting to other rape victims.

As for those women transsexual persons with gender recognition certificates who have been raped... I guess they're out of luck. The "Equality Act" is anything but.