On BioScience and Life and Such

Archive for May, 2008|Monthly archive page

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And now suddenly, we don’t need genetic counselors anymore…..?

In Uncategorized on May 30, 2008 at 12:16 pm

With this post, my posts on genetic counseling are now a trilogy (which somewhat unfairly puts them in the same category as some amazing literature, – and films).

From a recent Nature News Special Report:

No one denies that genetic test results can be life-altering for some individuals. But research by Theresa Marteau, a health psychologist at King’s College London, and others has shown that most people are remarkably resilient in the face of traumatic genetic test results. They typically report feeling anxious or depressed around the time of testing, but these effects dwindle within a few months.

This fits well with my first post where I argued that the need for genetic counselors was overrated. After reading an article on Huntington’s disease however, I changed my mind, and wrote another blog post. But now, this quote contradicts what I thought was my final conclusions and I am left wondering where I stand … again:

Studies by Aad Tibben, a psychologist and psychotherapist at Leiden University Medical Centre in the Netherlands, and his colleagues showed that people who took predictive tests for Huntington’s disease mostly recovered from the shock. Many actually felt more in control after testing because they could make arrangements for care, or even for euthanasia.

And I am not the only one who is confused on these matters

With so much uncertainty about how people deal with genetic risk, is genetic counselling necessary or helpful for people undergoing the less definitive tests for an increased propensity for heart conditions or diabetes? “I’m convinced it’s necessary,” says Tibben. But he and others in the field acknowledge that there is little in the way of controlled trials to support their belief.

I have decided to go with the conclusion that the best thing to do is probably to do the genetic counseling,… and then evaluate,… and then stop doing it if it doesn’t work. This simply because to my knowledge, genetic counseling doesn’t do any harm. It may even do some good even if the effect is all placebo:

“……….Did the counsellor help the patient understand complicated risks, or just provide some face-to-face contact and empathy in a confusing medical world?

So, until someone comes out with a study that says that genetic counseling is harmful, this post will reflect my final (!?) postition. End of story (trilogy).

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How everything is a mess and still ok

In Uncategorized on May 26, 2008 at 9:09 am


post to news.thinkgene.com

I have recently finished reading a Nature news feature on noise in gene expression (The Cellular Hullabaloo). It left me with this increased understanding of cellular processes and in terms of controlling chaos, fitted nicely with something I have blogged about before, which is Hsp’s (especially Hsp90).

According to this news feature, several studies have found that there are significant differences in the expression of genes both in duration and strength, even between cells that were expected to be identical. This contradicts the current notion of gene expression as an orderly sequential and structured phenomenon. These studies seem to indicate that gene expression occurs randomly, throughout the whole genome.

How these cells are still able to differentiate in a predictable manner,…… and perform specialized functions in concert with thousands of other cells,…….. to build a functional multicellular organism, is a mystery to me. And it is enigmatic to the researchers behind these studies as well:

“People are fascinated by how we do what we do despite this noise.” — James Collins

and

“People ask how come an organism works so well. Perhaps it doesn’t work so well. Perhaps organisms without these fluctuations would outcompete us.” – Johan Paulsson

How the noise came about and why it persists is still somewhat unclear, but benefits from such chaotic conditions may arise from:

1. Controlling randomness (noise) requires a lot of energy, the more chaos the less energy spent. Consequently, only the most critical cellular processes are under tight control, and the rest are more or less random.

2. Expression noise may enable cells to fight off threats. Say a certain level of protein is required to survive a toxic compound attack. Then having cells with sufficient levels of defender protein is more probable in a (noisy) cell population with varying gene expression levels, than in cell populations with a constant level of expression.

3. Randomness may ensure variation in differentiation. An example given in the news feature is the differentiation of blue and green light sensing photoreceptors in drosophila.

So, the noise is there for a reason. Noise, or more precisely – random fluctuation, is an ubiquitous cellular phenomenon. But cells of a given type still end up with similar morphology and similar functionality. The beauty of nature is how the randomness is controlled just enough to achieve the minimum amount of order necessary for preserving functionality. Also, in keeping the random events, flexibility is preserved for future adaptation.

The chaos extends further than gene-expression. If you also consider variations in insertions/deletions, gene copy number and epigenetic differences, the potential for random variation at the gene level becomes evident. To control some of this genetic randomness you have proteins like Hsp90 that masks genetic variation at the transcription level (or folding level to be precise). This is an important control-mode for some of the chaos (DNA sequence variation and mutations) and at the same time it enables sudden exposure of chaos to achieve rapid morphological evolution if needed. I am pretty sure that similar (or very different) control mechanisms will be discovered for gene expression noise in the future.

The noisy expression story is another illustration of how we are not just our genes. The DNA-sequence may be a defining starting point, but there are levels and levels of variation on top of that. As multicellular and evolving organisms, we are constantly balancing between chaos and order. The chaos-level is maximized to minimize energy expenditure and to ensure a multitude of possible paths to follow in an organisms future biological evolution.

The balance is oh so beautiful, it’s called nature.


Quote of the month

In Uncategorized on May 22, 2008 at 8:02 am

The May version of quote of the month comes from the CONCLUDING REMARKS in “Genomics and equal opportunity ethics” by A W Cappelen et al.:

“……….We have argued that genomics can provide us with information necessary to come closer to the ideal of equal opportunity ethics. Lack of genetic information has led to health policies that in some cases hold people responsible for too much and in some cases hold them responsible for too little. Recent advances in genomics may thus not only improve clinical practice and public health, but also help us to design fairer health policies………”

Note: quote removed from it’s original context (original article via PredictER News Brief) where also the dark side of the genomics age is elaborated on.

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New post on Sciphu.com, the advantages of blog publishing

In Uncategorized on May 19, 2008 at 8:54 am

There’s a new article on SciPhu.com. It’s about pharmacogenetics…..but what I really want to communicate is how superior this way of publishing is:

Here’s what I have experienced while blog-publishing:

1. It is fast. I decided I would publish some data that I already had presented in a talk, since this data wasn’t really fit for a major article. It took me an hour or so to write up and publish the whole thing.

2. One of the reasons it is fast is that it is less rigid in its form. You yourself decide on formatting, wording, whether to use a reference list and how to format this list, or if you would rather have your references as hyperlinks in the text.

3. Papers published on SciPhu.com get hits from google searches. Since the whole text is searchable the hit-probability for people looking for your subject is higher than that on pubmed or any other site where searches are based on title, abstract and keywords. An example is the gel-drying paper which is hit daily by google searches like “SDS-PAGE cracking” or “vacuum drying PAGE” or similar. Although in this case, you could surely search laboratory method web-sites, the fastest way to find your information is probably a google search. This means that any paper published like this has the potential of high visibility. In addition you can get day by day hit statistics, which is probably interesting to many.

4. Communication with referees is interactive and the paper can remain fluid in its format and content. Since publishing like this is rapid it is also bound to be more error-prone. But, by interacting through the comments section, the paper can be continuously revised to correct errors or unclear phrasings. Also the number of referees can be many and since everyone can see the referee-comments, replying to these referees can be done by anyone, not only the authors. Thus, the papers will be less perfect to start off, but may end up better than those in a traditional peer review journal.

5. It is open access and free to everyone. Anyone’s welcome to publish anything as long as it is scientific. This is true scientific democracy.

7. SciPhu.com lacks the “rigid editor” entry point, and it always will.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many of us scientists are willing to use publishing channels like these, will it become a success.

This is the age of the web and no-limit communication accessible to all. My recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

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Updated Normality

In Uncategorized on May 15, 2008 at 3:15 pm

Just to remind myself:

Something “Constant” exists only on paper or in silico.

In life “Normal” = Variation

Variation can be Random or have a Trend, but even the Trend Fluctuates and is never Constant.

If this is true then the terms “Constant” and “Life” are incompatible. And consequently, “Living a Normal Life” cannot possibly be Defined.

Updated from previous post “Normality“


Diving into Transhumanism II

In Transhumanism on May 14, 2008 at 3:23 pm

Endpoint: Become a Transhumanist or not.

In the previous posts Epiphany: Transhumanism, not ? and Diving into Transhumanism I, I have introduced the Transhumanist philosophy as presented on the World Transhumanist Association (WTA) website. This post will look at some examples on how transhumanism translates into real life in the foreseeable future (the quotes are still from the WTA website).

Drugs

Life-events have little long-term impact; the crests and troughs of fortune push us up and bring us down, but there is little long-term effect on self-reported well-being. Lasting joy remains elusive except for those of us who are lucky enough to have been born with a temperament that plays in a major key.

Drawing from the (depressing and hopefully untrue) quote above and other potentially drug-promoting statements on the WTA-web, one would assume that the safe use of mood-changing drugs (and cognitive enhancing drugs) must not only be accepted beyond recreational use, but also recommended to everyone to achieve lasting happiness and increased mental capacity. The pitfalls here are more than obvious however, and the lack of a solution on how to avoid detrimental drug abuse is a major drawback. Drugs are meant to treat disease and the dangers of pushing for extended use in the general population are evident to everyone. If being a Transhumanist means pushing drugs to otherwise healthy people, I need to pass.

Artificial intelligence

Transhumanism promotes accepting artificial intelligence (AI) and supporting it’s widespread use. This I guess, could be a good thing. But, as I will come back to in a later post, many Sci-Fi scenarios are situated in a machine-run future where humans have lost control. The Transhumanist values seems to reject the possibility of such a development since one of the Transhumanist values is to give equal rights to future sentient AI machines.

Should future forms of artificial intelligence
become sentient, they would be entitled to
moral consideration. Nobody should be discriminated
against on the basis of their morphology or
the substrate of their implementation.

Like in the case of drug use, this is naive in my opinion. Is it plausible to believe that we in the foreseeable future can design sentient AI that display the compassion, care and love it has taken biology millions of years to develop. Such an advanced morality must be a prerequisite for equal rights. Reassuringly though, there is a section on the dangers of AI which shows that Transhumanists see the dangers of their own philosophy.

As the prospect of general machine intelligence draws closer, more thought needs to be devoted to working out the legal, ethi-cal, social, and security implications, e.g. to deter-mine under what conditions artificial intellects or copies of existing persons should be given property rights or voting rights, and whether new public poli-cies will be needed to ameliorate structural unem-ployment.

Infertility and Cloning

Any procedure to create healthy offspring is supported by Transhumanists. That means that widespread use of in-vitro fertilization (IVF) and other assisted reproduction technologies (ART) is encouraged. On a positive note, I have already changed my attitude towards IVF based on my ongoing Transhumanism studies. But, to revert to the more questionable Transhumanism values, preimplantation genetic diagnosis (PGD) must also be supported (since the endpoint is a better, healthier human being) and worryingly for a lot of us, reproductive cloning is equally supported and encouraged. I have posted on the slippery slope of PGD previously, and it is no secret that I have have serious problems accepting extended use of PGD. On reproductive cloning It is argued that opposition to human reproductive cloning (HRC) can be described like this:

….objections to HRC are based on the “yuck factor” — it just “feels wrong” to some. But our right to control our own reproduc-tion, not to be told by the government what kind of children we should and shouldn’t have, is far too important to be determined by other people’s vague anxieties. We learned that from the terrible history of eugenic laws. Historically the same people who say that HRC is wrong said the same thing about IVF. Just as society got used to the idea of “test-tube babies” so we will also get used to the idea of cloning.

Now, it may be true that there is a “yuck factor”, but dismissing the rather unison opposition to HRC on account of this is not only arrogant, but also non-scientific and down right unintelligent. Of course there are plenty good arguments against reproductive cloning. From a biologist perspective I worry that genetic diversity will suffer if cloning becomes common. There are benefits to sexual reproduction. Thus, the evolutionary consequences of cloning could be devastating. In addition, there are plenty more, perfectly valid counterarguments, – here are some taken from Center for Genetics and Society:

1. Reproductive cloning would foster an understanding of children, and of people in general, as objects that can be designed and manufactured to possess specific characteristics.

2. Reproductive cloning would diminish the sense of uniqueness of an individual. It would violate deeply and widely held convictions concerning human individuality and freedom, and could lead to a devaluation of clones in comparison with non-clones.

3. Cloned children would unavoidably be raised “in the shadow” of their nuclear donor, in a way that would strongly tend to constrain individual psychological and social development.

4. Reproductive cloning is inherently unsafe. At least 95% of mammalian cloning experiments have resulted in failures in the form of miscarriages, stillbirths, and life-threatening anomalies; some experts believe no clones are fully healthy. The technique could not be developed in humans without putting the physical safety of the clones and the women who bear them at grave risk.

5. If reproductive cloning is permitted to happen and becomes accepted, it is difficult to see how any other dangerous applications of genetic engineering technology could be proscribed.

Their pro and con site has more on this issue, – worth reading. In light of these counterarguments it is very clear that WTA is on thin ice when they are dismissing the whole debate based on the “yuck factor”. This better not be symptomatic in their dealings with issues of this importance.

The disabled

I am ending this post on a positive note, since those who can benefit most from biology-enhancing/repairing technology are the disabled.

Disabled people in the wealthier industrialized countries, with their wheelchairs, prosthetic limbs, novel computing interfaces and portable computing, are the most technologically dependent humans ever known, and are aggressive in their insistence on their rights to be technologically assisted in fully participating in society.

Any technology that enables interaction and inclusion in society whenever that would otherwise have been impossible, cannot possibly be opposed by anyone. But, the disabled must not end up as guinea pigs for tech-testing, and the right to refuse to adopt technologies must be central. Giving WTA extra points on this issue is this statement:

Just as we should have the choice to get rid of a disability, we should also have the right to choose not to be “fixed,” and to choose to live with bodies that aren’t “normal.”

Other cons for still considering Transhumanism includes their expressed intent to care:

about the well-being of all sentience

And most importantly, their open-debate approach to science and ethics. Not all emerging philosophies in history has had these as core values, and that may have been why so many of them brought about such devastation and human grief. If you on the other hand combine heartfelt intention to do good with open debate and a willingness learn from such a debate, you may have a winner…….even if your original views where completely off base.

More to follow.

Trading places

In Uncategorized on May 8, 2008 at 1:48 pm

Here’s an easy way of setting things right when they are obviously wrong in the first place. Just do a switch !

This is a quote from a disturbed person taken from nature news sidelines:

“Love of God and compassion and empathy leads you to a very glorious place, and science leads you to killing people.”

Setting it right by switching God and Science:

“Love of science and compassion and empathy leads you to a very glorious place, and God leads you to killing people.”

Now, when the right order is restored like this, the statement is almost divine in it’s simplicity, isn’t ?

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Ok then, everyone can have IVF….

In Uncategorized on May 6, 2008 at 8:33 pm

I have clearly entered an argue against myself phase, and since reading this article quoted on Genomeboy pushed me further into this “disagree with self” state, I am going to argue against another one of my posts.

In a previous post called “Should public health care pay for IVF-treatment ?” I argued that public health care, with its limited resources, should not prioritize ART/IVF, especially not in developing countries where health resources can be very limited indeed. This spurred a lengthy discussion with Faith over at Invisible Grief. I must admit that I learned a lot from that discussion. Now, since I am also considering Transhumanism, it is time to reevaluate where I stand on this subject. Transhumanism is all about giving everyone access to biomedical technology and also about embracing the widespread use of such technologies to enhance our biological selves.

Whatever I may land on on Transhumanism however, I have reached the conclusion that everyone should have access to ART/IVF. This I guess, is in contrast to arguments in my previous post.

……But, I still think that this treatment should be financed separately (outside of the public health budgets), either through dedicated public funds or privately. Such a separation will clearly state that ART is a desired medical technology either as a part of a policy on reproduction for everyone or as a part of a womens rights plan. The key criterion for such an endorsement of ART/IVF must be universal and unrestricted access to assisted reproduction technologies for everyone.

….Accessible to everyone………herein lies the crux…….Answer: It must be publicly funded. Thus, I stand corrected (by me), – again.


Diving into Transhumanism I

In Transhumanism on May 2, 2008 at 7:34 am

Endpoint: Become a Transhumanist or not.

This first post records my introduction to Transhumanism. Emphasis is put on counter-arguments as the transhumanist texts can be as alluring as those of a religious sect. This skepticism creates an objective barrier protecting my feeble (subjective and feeling) soul.

On the World Transhumanist Association website theres a section called “Transhumanist values“, divided into 5 sections:

1. What is transhumanism.

It promotes an interdisciplinary approach to understanding and evaluating the opportunities for enhancing the human condition and the human organism opened up by the advancement of technology

Both present and future (yet unknown or emerging) technologies are included. Also included are terms normally associated with Science fiction, like space colonization and the creation of superintelligent machines as well as cryonics. All this, while certainly sounding weird and strange, I guess is harmless. Harmful potential however, emerges from….

an evolving vision to take a more proactive approach to technology policy. This vision, in broad strokes, is to create the opportunity to live much longer and healthier lives, to enhance our memory and other intellectual faculties, to refine our emotional experiences and increase our subjective sense of well-being

These all sound like good values, but it’s important to note that they contain problematic issues like cloning, human sorting, drug use and abuse, and lastly, but most importantly, the hard to avoid increase in social/intellectual/health inequalities between those with resources to access the technology and those without such resources.

2. Human Limitations

The range of thoughts, feelings, experiences, and activities accessible to human organisms presumably constitute only a tiny part of what is possible.

Which is probably true. The goal is to increase access to these yet unknown layers of the universe. A mind boggling perspective, – and an intriguing one too.

It is not farfetched to suppose that there are parts of this larger space that represent extremely valuable ways of living, relating, feeling, and thinking.

It is equally not farfetched however, to assume that there are parts of this space which will prove to be highly unattractive, or even dangerous to us. Also as I will touch upon in later posts, the means of enhancing cognition have inherent dangers especially if drugs are involved.

3. The core transhumanist value: exploring the posthuman realm. The desired endpoint of Transhumanism is the “posthuman” being, which will probably be markedly different from our present existence. The time in between us as human beings today and the posthuman being, the world will be populated by transhumans. Foreseeing the features of the posthuman being and finding ways to get there, is what transhumanism is about. The labels that Transhumanism puts on these processes however, are only fancy names for evolution in a modern technology driven world. No need for a separate ideology to see that the future human will be different from he present one. Nevertheless this vocabulary can prove useful in discussions on ways to responsibly achieving a better future.

4. Basic conditions for realizing the transhumanist project. This section outlines the dangers of uncritically embracing progress in technology. Restricted access to the technology is mentioned as one danger, global security (where the need to ensure sustainable development is underlined) is another one. A new technology should not be used if it poses…

Existential risk – one where an adverse outcome would either annihilate Earth-originating intelligent life or permanently and drastically curtail its potential.

And that is reassuring to me. Still, on a negative note, I do feel that this section on possible dangers is suspiciously short compared to the other sections.

5. Derivative values. For the individual, these are freedom, individual choice, education, critical thinking and open-mindedness. A caution is added:

In cases where individual choices impact substantially on other people, this general principle may need to be restricted, but the mere fact that somebody may be disgusted or morally affronted by somebody else’s using technology to modify herself would not normally a legitimate ground for coercive interference.

These are values I can easily identify myself with, but maybe one should caution also that individuals should be protected from themselves. Receptive, uncritical individuals lacking suitable knowledge in a given field will be in real danger when presented with hyped up inventions (personal genomics is an example). Common values on the other hand include research, public debate and open discussion. It is stated that collectively…..

We will need all the wisdom we can get when negotiating the posthuman transition.

How this wisdom is to be applied as a a normative social superstructure is not specified though, and this is clearly a challenge.

In summary, my impression of Transhumanism is divided between the still prevailing enthusiasm and (what I now find as) justified skepticism. It seems clear to me that the implementation of these ideas needs a solid, commonly accepted social framework to avoid negative repercussions. That said, such a framework may not be impossible to carve out.

More quotes to end this introduction:

“Transhumanism is a philosophical and cultural movement, not a religion. Transhumanism does not offer answers about the ultimate purpose and nature of existence, merely a philosophical defense of humanity’s right to control its own evolution. Consequently the transhumanist philosophical stance is compatible with humanist interpretations of the world’s religions.

On the other hand, transhumanism is generally a naturalistic outlook and most transhumanists are secular humanists. Although scientific rationalism forms the basis for much of the transhumanist worldview, transhumanists recognize that science has its own fallibilities and imperfections, and that critical ethical thinking is essential for guiding our conduct and for selecting worthwhile aims to work towards. Religious fanaticism, superstition, and intolerance are not acceptable among transhumanists.”

The following posts will dive deeper into the depths and specifics of the philosophy. And the final decision on becoming a Transhumanist or not still remains…….