On BioScience and Life and Such

Archive for January, 2008|Monthly archive page

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On ScienceBlogs 27/-1-08: Quick-Change Evolution

In Uncategorized on January 27, 2008 at 9:46 pm

I have so much to learn, and I’m looking so much forward to learning it. This time around it’s in evolution theory, and I’m going to make some bold statements while learning.

Some recent posts here on SciPhu has been on Hsp90 and rapid morphologic evolution. On ScienceBlogs the topic of the day is Quick-Change Evolution. The background is a blogpost by Olivia Judson stating the return of the hopeful monster. The hopeful monster theory says that extensive morphologic changes in one individual offspring (a monster – an individual organism looking radically different from the rest of its species), sometimes creates beneficial features enabling the monster to create further offspring with similar features. In this way one can achieve rapid evolution (as short as one generation) into the beginning of a new species. The theory is a controversial one and is also called punctuated equilibrium. I however, am apparently at odds with most science bloggers and evolutionary biologists, since the hopeful monster theory sounds plausible to me. How is this linked to Hsp90 you may wonder. Well…

Knocking down Hsp90 creates rapid morphological changes from one generation to the next (for details see references in my previous posts Evolution too fast for our genes to follow, On Hsp90 and morphological evolution and The rate of evolution/mutation/adaptation and future posts to come). Hsp90 does so by masking mutations under normal conditions and then revealing them under stressful conditions. Just to repeat myself, – this concept suddenly made evolution comprehensible to me, and I do not understand why other scientists haven’t embraced the masking concept as a revolutionary concept, expanding darwinian evolution theory.

Now it’s dawning on me why…….Such masking of mutations to produce a pool of potentially crucial mutations gives support to the hopeful monster theory.

One of the main criticisms of this theory, as far as I can understand, is the improbability of a single mutation to give rise to radical morphological changes, and further that this change, if it happens, is most likely deleterious, and if it against all odds is beneficial, its even more improbable that this individual is able to produce offspring with the same trait(s). But…..

Extensive morphological change has been shown to happen due to single mutations, and…

With Hsp90 as a player in the game, it need not be a single mutation, but rather a pool of mutations already present and waiting to be exposed under stress. That increases the chances of achieving multiple changes in multiple individuals. Consequently the chance(s) of producing one or more beneficial trait(s) is(are) increased.

In addition, if such stress appears and mutations are revealed, then many individual offspring will have extensive changes, and the chances for two such individuals to mate increase dramatically.

Thus, I cannot see why a combination of the hopeful monster theory and the actions of Hsp90 (and possibly other mutation masking proteins) under stressful conditions, is a perfectly credible extension to darwinian evolution. An extension that can explain some of the rapid changes that has occured during evolution of species.

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A refreshing view on James Watson

In Uncategorized on January 23, 2008 at 12:23 pm

On the Honest Thinking website there is a post that comments on the unison negative response to James Watson’s remarks on race when interviewed by The Independent.

As many will remember the interview created a general outrage and Watson was suspended from his job. There is no doubt that his phrasing was not very delicate, to put it mildly. The subsequent reactions from the politically correct masses were perhaps justified since traces of racism could be found between the lines in his remarks (as well as in previous public comments by Watson).

But, what is the science behind it all ? This popular article shows us that there’s more than one side to this story. It seems that there is solid scientific evidence to support the alleged IQ-difference between blacks and whites. Importantly though, the reasons for this difference is currently not well understood. And even more importantly, genetics is probably only partly to blame.

The way such data is presented is crucial to how it is interpreted and used in a political world. Matters of race awakens strong emotions in us. To avoid misuse of scientific data, it is important to carefully present results concerning race as unbiased and delicately as possible. The motto taken from Honest Thinking: “…….being truthful about whatever one publishes, …….. uncompromising dedication never to suppress relevant data, even when data collides with dearly held prejudices.” is commendable, but fails to account for the presentation itself. The presentation was in this case, equally or even more important than the data, – a lesson hopefully learned by Professor Watson.

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10 ways to use your DNA

In Uncategorized on January 18, 2008 at 7:59 pm

Not really news, but for a long time now, I have been meaning to compile a list of different more or less useless DNA-technology applications. Although some may argue that some of these applications can be very useful for the individual, and that some of these sites have yet to reach their full potential, I still think these sites share a general uselessness in improving society.

The list is unsorted.

1. Hairloss. But what difference does it make whether you order a toupée sooner, or later ? Maybe it gives you time to save up for your favorite hairpiece, …….although since you spent your savings buying the test ……..

2. Dogfood. Especially formulated fodder to fit your dogs genetics, – probably including proteins, carbohydrates, fat, sugar, vitamins, minerals and salts – it’s a revolution !

3. Several companies offer genetic testing to optimize your diet and lifestyle. This company and this one are examples. You can also order a genetically optimized juice here and your supplements here. Unfortunately I suspect that the advice we all know already, enough exercise and healthy eating habits, is pretty much the advice these companies are going to give you too. Besides most of us know which foods we tolerate or don’t.

4. Personal genetics from 23andMe, Navigenics and DeCodeMe. This review comments better than I would have, on the health benefits or lack thereof. However, these companies may very well provide very useful genetic information for future research. Whether you should pay $999 for this is another question. Maybe join this project instead ?

5. Genetic ancestry. This is a small industry now. Here, here, here and here are examples. A skeptical news story can be found here. Since Oprah has endorsed these tests, they will prevail, – much like the American presidential election campaign 2008 is settled already, seeing that Oprah has given her support to Barrack Obama.

6. Another emerging industry is paternity testing (examples here, here and here). Actually, this is arguably a useful application for some. Getting knocked up and opting out of abortion, will never be the same.

7. Stretching paternity testing into detecting extramarital affairs however, is definitely not very useful. Is it infidelity you discover or just someones DNA somewhere ? This is the essential question, – usually answered in lengthy court trials and not in any given household.

8. Cosmetics. The following genes will apparently be analyzed in this test: MMP, SOD2, GPX1, EPHX, TNFa. These genes encode proteins central in many cellular processes, not confined to skin cells. Assigning them the responsibility for skin “health” is therefore stretching it. My point is underscored by the fact that the same genes (with some additions) are analyzed in the same company’s…

9. Aging panel (genes: MMP, SOD2, GPX1, EPHX, TNFa, VDR, NQO1, MTRR, MTHFR, PON1, Cyp11B2, ApoB). But if determining aging was this easy then what use are efforts like these.

10. Breeding – DNA-testing is used extensively and increasingly in breeding programmes for livestock and horses. In itself useful I guess, but using this to determine your dog’s breed seem to me to be more on the useless side. Most breeds I know are distinguishable by the naked eye, and usually when you buy a dog from a breeder, the complete ancestry is given. Keeping the ancestry logs and consequently having a pure breed, is what breeders make a living out of.

The first version of this post was published here (not in English).

Metabolomics and the microbiome

In Uncategorized on January 16, 2008 at 12:08 pm

This article from ScienceNow is interesting. When we have characterized the micro organism communities within our bodies, we may start manipulating them into combating disease as well as life style ailments.

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At ScienceBlogs: Why don’t they make a birth control pill for men?

In Uncategorized on January 10, 2008 at 8:39 pm

In response to the various answers to this question at ScienceBlogs: Here’s a company that you may find interesting. They are working on a non-hormonal male contraceptive alternative. The drug target is a sperm specific protein that is apparently crucial for motility. Cool if they can make such a drug work, – but even if they can, will men use contraceptives ??

According to this site, – yes, and they even list a number of places where clinical trials are happening (although not for the spermatech drug candidate), – trials you could join presumably, if interested, for some reason or other.

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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.