On BioScience and Life and Such

Archive for the ‘Uncategorized’ Category

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Ethical obviousness

In Uncategorized on January 9, 2008 at 3:27 pm

Just to clarify. Even though I sound like an opponent of genetic testing in my previous post………….. I’m not. And to emphasize this, here’s a quote that I sympathize with, from this post at genomeboy: “When people ask me whether I’m nervous about getting my DNA sequenced, my response is always the same: “My genome is the least of my problems.””

Although one could argue that since your genome is your be-all then your genome is your only problem, alternatively that you have no problems since your genome is you and yours..(……..sentence ended up in philosphical jibberish….)

Take home message: DNA-testing of consenting informed adults is fine for any test, – but ethical care should be taken when used in in prenatal care or in pre-symptomatic diagnostics of children unable to give their own informed consent….(…paragraph ended up in ethical obviousness…..)

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Tests that make me sad

In Uncategorized on January 7, 2008 at 9:45 am

In a previous post (“Clarifying misuse of Science“) I expressed concerns over Prenatal testing for familial hypercholesterolemia. Now it seems I should have included two more (and in my mind, – more controversial) tests approved in the UK for preimplantation testing preceding IVF. These are tests for breast cancer (BRCA1) and early onset Alzheimer.

I must have been naive to oppose the slippery slope argument in genetic testing discussions up until now. I wish we could restrain ourselves a bit more, but fear that we can’t. Why haven’t there been more fuzz around this ? Is everyone going to switch to using prestested eggs in IVF now ?

A (tricky) solution is to come up with treatments for most of these conditions, – looks like that needs to happen fast if we’re to avoid the brave new world future that critics of the genetics era have been promoting …..

The “find a cure” process of course, is not going to be fast and in the 10-25 years to follow, those concerned couples that have this option will most likely not take the chance that a treatment will be found in time for their child to be cured, and opt for the safer pretested egg and IVF.

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The rate of evolution/mutation/adaptation

In Uncategorized on January 3, 2008 at 1:48 pm

I came across this blogpost from evolgen which is a part of a discussion with John Hawks on increased rate of evolution. It seems to me that the term “neutral mutation” is central in this discussion. However, looking at the effect of Hsp90 as described in my previous posts (and future posts to come), – is it possible that some of these “neutral” mutations aren’t neutral at all, but rather deleterious or beneficial mutations masked by a heat shock protein ?

I am in over my head when it comes to in-depth analysis of population genetics data, but still, to me, – the action of mutation masking Hsp’s (if this is truly a valid evolutionary phenomenon) may seem to bridge these two opponents as well as solving a lot of other controversies surrounding the rate of molecular evolution vs. phenotypic/morphological evolution.

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A qoute to guide us

In Uncategorized on January 2, 2008 at 1:45 pm

To start off 2008, here’s a quote that I feel everyone in Science should take ad notum. The section is taken from the bbgm blog.

“It is very easy for us to believe, as scientists, that science is the be all and end all, and anything that diverges from hard science is not to be taken seriously. However, over the past few years, I have come to realize that such an approach only results in alienation and a barrier between science and society. My mind on the importance of science in society and for our future has not changed one bit. What has changed is how it fits into the fabric of our future. In a world full of inequality and agendas, our conversation with the world, as scientists and scientific thinkers, should focus on making science more accessible. Does that mean we compromise on the quality of our science? Absolutely not, but we should not be naive enough, or perhaps arrogant enough to think that just because we have fact on our side, everyone is going to subscribe to our point of view.”

Very well put ! I have become a fan. I also think these arguments are in line with my thoughts on Dawkins in the previous posts.

On Hsp90 and morphological evolution

In Uncategorized on December 21, 2007 at 12:05 pm

As a further introduction into Hsp90 and its role in evolution, here are two segments cut from this review:

1. “Because signaling proteins with multiple regulatory states often undergo a conformational switch, the structural flexibility needed for these steps may render them inherently less stable and thus more likely to be recognized by Hsp90. On the other hand, under stress conditions such as heat shock Hsp90 contributes more generally to the refolding of denatured proteins (Nathan et al., 1997). Although the exact structural features recognized by Hsp90 are not yet understood, the exposure of these features to Hsp90 is likely a result of intrinsic or stress-induced structural flexibility. Thus, interactions of substrate proteins with Hsp90 arise from structural properties at the molecular level rather than biological function.”

2. “Defects in cell physiology caused by Hsp90 disruption can lead to defects at the level of tissue and organism. Interestingly, recent work connects Hsp90 function with morphological evolution, a process that often requires the effects of independent genetic changes (Rutherford and Lindquist, 1998). Hsp90-null mutants are lethal in eukaryotes, but surprisingly partial disruption of Hsp90 in Drosophila by a temperature-sensitive mutation or low amounts of GA shows a wide assortment of heritable phenotypic variations. The variations may arise from alleles of proteins, which depend on the full function of Hsp90 as a conformational buffer to maintain “wild-type” activity but whose phenotypes can be stabilized by other genes following selection. By extension, polymorphisms in all of the proteins participating in an Hsp90-dependent signaling pathway should be buffered by Hsp90 function. In the wild, overloading of the Hsp90 “capacitor” with denatured proteins under environmental stress could similarly increase the phenotypic diversity on which natural selection and ultimately evolution acts (Rutherford and Lindquist, 1998). Hsp90 with its connection to the cellular signaling network may be particularly suited to such a function. Thus, the mechanisms of chaperone-mediated protein folding at a molecular level can be integrated with cellular processes and with the development of organisms and species.”

Thus, if I understand this correctly: Under stressful conditions the Hsp90 is titrated away from its normal substrates exposing structural variations otherwise masked. Seeing that many of these normal substrates are signaling proteins (and thus affects many other proteins) this potentially, leads to extensive variations in phenotype.

More to follow

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Evolution too fast for our genes to follow

In Uncategorized on December 20, 2007 at 1:41 pm

In the near future, the upcoming posts will center on Heat shock protein 90 (Hsp90) and how the function of this particular protein can explain rapid morphological evolution, or rapidly evolving phenotypic variation if you will. The topic and papers on it, are in my opinion hugely underrated. To me, until these papers came out, the extremely rapid (in a cosmic timescale) change in physical appearance that is seen in the evolution of species, was the major (only ?) valid argument contradicting Darwinian evolution through random mutations and genetic drift. This because genetic drift through random or even guided mutations, is just too slow to explain the evolution of such a vast spectrum of species as the one present on earth, in such a (relatively speaking) short time. The concept of masking mutations through the action of Hsp90 was an eye-opener and presented me with an extension to genetic evolution that explained rapid phenotypic change. Thank god(!) for this possible counter argument towards the missing link babble presented by creationists and their like. And it is surprising that these papers haven’t been used more in discussions concerning evolution. More details on Hsp90 to follow, but the fundamental paper is (not open access unfortunately): Hsp90 as a capacitor for morphological evolution Nature 396, 336 – 342 (26 Nov 1998).


Clarifying Misuse of Science

In Uncategorized on December 17, 2007 at 2:53 pm

Just to expand a little on the subject, in our previous post, of misusing science. There are two ways of misusing (abusing ?) science. The first is twisting scientific facts to fit ones own agenda. The other and more immediate, way of misuse is achieved when ethics is left behind in practical applications of science. Prenatal testing for familial hypercholesterolemia is sad recent example of the latter.

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Richard Dawkins beeing clever on hindsight

In Uncategorized on December 14, 2007 at 10:14 am

Something that should strike anyone reading, or listening to, Dawkins arguments against religion is: Beeing clever on hindsight is always easy.

It is easy to see that God and religion are delusions (or faith as one might call it) knowing what we know today. Throughout history however, alternative explanations to existence has been sparse or non-existent and religion has been the best explanation anyone has been able to come up with. Consequently all known societies has had one or more Gods. Religion has been at the root of building society as we know it today, including the flaws.

Today, science builds society more than religion does, – and increasingly so. Science is therefore at risk of becoming the new religion, and Dawkins may be destined for one of the new Archbishops. We should all learn from the history of religion and avoid the pitfall of discrediting and ridiculing what we cannot explain or things we cannot find supporting evidence for. What science cannot explain today, including any superhuman beeing or force, is not necessarily wrong to believe in, and explanations or evidence for some kind of a God may appear in the future when scientific knowledge explains the currently hidden details.

Instead of concluding the obvious (that God is a delusion), we should take Dawkins arguments as strong documentation for the continuing misuse of religion to opress and abuse. This misuse is not due to faith in itself, but rather blaim should be put on the people claiming religious leadership and authority. These peoples actions are probably more a result of darwinian principles (as the struggle to excede other members of a population, – through oppression or otherwise, is a fundamental darwinian principle), than they are results of religious faith.

This last point is important to remember because science will inevitably be misused the same way, and we as scientist are obliged to fight back.

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The need for restraint

In Uncategorized on December 12, 2007 at 1:32 pm

Overselling Science is probably the biggest threat to scientific credibility, nevermind cheaters like Hwo Suk Hwang or even intelligent design. These are obvious and passing threats, easy to neutralize. Rather, do mind genetic genealogy companies telling you they can find your extended family (when what they actually find is your haplogroup), personal genetics companies telling you about your lifestyle and disease risks (when these risks are low and penetrance is uncertain), – and mind greatly: dating companies telling you they can find your match based on your DNA-profile.

We are moving in the right direction, let’s not screw it up for ourselves.

Normality

In Uncategorized on December 11, 2007 at 1:52 pm

Normal is variation, no exception.