On BioScience and Life and Such

Posts Tagged ‘scientific method’

They say men haven’t evolved towards domestic use

In Uncategorized on September 10, 2009 at 2:11 pm

post to news.thinkgene.com

Male symbol. Created by Gustavb.

Image via Wikipedia

First off, I have to admit that my scientific knowledge is a bit sketchy on this one. Nevertheless – my impression is that there is a (scientific ?) consensus out there saying the following:

The nature of men is that of the restless promiscuous hunter. Evolution has provided pressure towards maximizing the spread of male genes through procreating with as many women as possible. This way the number of offspring one man can obtain is maximized. Apparently observations supporting this view are the vast amount of sperm cells produced in the male reproductive organs and the continuous (not cyclic) nature of this sperm-production. The logic is, I think, that the production of all these sperm cells would be futile if destined for only one woman with a cyclic reproduction cycle. So far so good.

Consequently, the masculine “nature” is continuously compromised in our modern monogamous lifestyle. Male infidelity is often excused using the arguments above. The same arguments also makes domestic life and caring for the family into a compromise with “natural” masculinity.

Still good ?

Even if making as many offspring as possible seems like a good strategy to pass on (male) genetic material, isn’t it possible that another strategy would work just as well.

You could argue that continuous sperm production is present to counter a single woman’s unpredictable cycle, – or compensate for miscarriages, – or compensate for children born by this woman dying young (not so rare in those older days). This make-one-woman-pregnant-many-times strategy could potentially lead to as many offspring, themselves reaching reproductive age, as the multiple partner strategy.

If you buy into that last argument, there is no reason why the selective pressure on men has been towards domestication and taking maximal care of his one-woman family. And, against inclination towards infidelity.

I’m so sorry for ruining our excuses here my fellow men, but the whole man-as-a-hunter-excuse has been bugging me for a long time. I find it hard to understand why such an idea has been elevated to universal truth. I believe a need for behavioral excuses has overridden scientific rigor on this one. Anyone who can convince me otherwise is more than welcome.

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The universal PEG

In Uncategorized on July 1, 2008 at 12:00 pm

The most popular publication on SciPhu.com is on gel drying of SDS-PAGE using Poly-Ethylene-Glycol (PEG). PEG is used in many industrial applications as well as in research-experiments in the lab. Now Nature news reports that PEG may have a (distant) future in Medical applications as well. The nature News piece quotes Richard Borgens of Purdue University saying PEG acts by:

absorbing water, promoting the healing of cell membranes and preventing “the exchange of things that cause decay and degeneration of the cell”. Once it reaches human trials, PEG could be carried by trauma units and administered as soon as emergency crews reach victims of blunt-force trauma.

Especially the phrase

…..preventing “the exchange of things that cause decay and degeneration…..

,..appeals to me.

Hurray for PEG, – and may I remind you that using monodisperse PEGs (PEGs with a defined mass) increases the accuracy and reproducibility of anything you would want to use it for.

Was it all in vain ? The scientific method tale

In Uncategorized on June 23, 2008 at 9:34 am

post to news.thinkgene.com

I did my PhD on one of the most studied enzyme-systems of all time, the cAMP-dependent protein kinase (PKA). One would think that the tools we used were accurate when the enzyme was as thoroughly characterized as it was. But alas!, now we learn they had major flaws. The endless kinase assay’s lasting until the wee hours, were they all in vain ?

“….nonspecific effects are
widespread; they include actions on other protein kinases and signaling
molecules and also on basic cellular functions, such as transcription.”

We had two teams in my group, one was the gene characterizing team – we did cloning, sequencing, expression and transcription analyzes mostly. The other was the protein activity and interaction team who did a lot of enzyme activity (kinase) assays, protein-protein interaction and immunoblots. Members frequently crossed team borders to learn the necessary methods. I was in the gene-group, but I did my occasional kinase assay and cell-culture experiment as well. As a rule, the kinase assays (as well as cell culture assays) always included inhibitors of the kinase and very often those inhibitors were H89 and/or  KT5720. These inhibitors were thought to be specific so that any decrease in enzyme activity one would see upon adding them, was attributed too a loss of PKA activity.

A recent review by Andrew J. Murray in Science puts a serious dent in that assumption. These inhibitors seems to act on a range  of other signaling systems. Their targets seems to be very diverse indeed. Specific they most certainly are not. That means that a lot of the inhibition we would see and base our conclusions on, was wrong.

“…a substantial
body of evidence has now accumulated
that indicates that both H89 and KT 5720
can have effects independent of PKA inhibition.
These actions are extremely varied;
some of the most worrisome actions are the
substantial effects on the MAPK and calcium
signaling pathways, which interact with
the PKA pathway and mediate multiple
cellular functions.”

and even more worrying:

“Furthermore, many of
these non–PKA-based actions of H89 and
KT 5720 occur at concentrations that have
been widely used to investigate PKA function.”

The final conclusions and the cellular mechanisms we unraveled, one can only hope were not wrong, which would be fortunate for me and others with a history in the field. But, one can never be sure and reevaluation may be in place for some of the past studies

“the molecular bases of some
cellular processes attributed to PKA solely
through the use of these compounds may
have to be reevaluated.”

Any experiment with H89 in the future needs to take this new information into account. And in the review, the author outlines a number of alternative approaches to inhibit PKA activity in a specific manner.

The above outlined studies indicate that neither
KT 5720 nor H89 should be used alone
to study the function of PKA. As these compounds
are so commonly used, it will therefore
be necessary to devise strategies that
can overcome their shortcomings.

Although annoying and possibly detrimental to papers I have published in the past, I cannot help having this proud feeling. Because, this is the beauty of the scientific method: not only do we admit we’re wrong (and publish it in high impact journals), we have efficient methods to prevent the wrongdoings from continuing. Any responsible and updated reviewer will now dispute all conclusions based on experiments involving these inhibitors. Then scientific results in the field will become more accurate. In addition, new conclusions and insight may come from this increased understanding of the limitations on previous results.

Science involves unrestricted sharing, regardless of the nature of the information. Add peer-review and you have  the scientific method working at its best.