Genome Biology - Latest Comments

Hypomethylation may change Alu transcription level

Dajun Deng — 2010-03-15T00:00:00Z

It is interesting that expessed Alu repeat may be a good reference for transcription normalization of target genes. However, it is well known that Alu elements in the human genome are hypomethylated in many cases such as cancer tissues and tissues exposed to cytotoxic chemicals and anoxic conditions. It is likely that transcription activity of Alu elements may change due to the hypomethylation, which might reduce the proposed normalization value of Alu transcripts. It will be useful if authors could exclude effect of the hypomethylation on Alu transcription.

The conference website

Jerzy Jurka — 2009-04-23T00:00:00Z

More details about the conference, including the book of abstracts can be found on our website:

http://www.girinst.org/conference/Asilomar-2009/index.html

Correction in Table I

Silvestro Conticello — 2009-02-16T00:00:00Z

In the table the localization of APOBEC3A and APOBEC3B were inverted. This has now been corrected.

Correction

Thanya Nirantasook — 2008-08-14T00:00:00Z

In the legend of Figure 3 parts (a) and (b) were incorrectly described as (a) CRLMM and (b) BRLMM in the final version of the paper. This has now been corrected.

Separating racist judgement from scientific objectivism

John Copen — 2008-07-30T00:00:00Z

There is no doubt there are both phenotypic and genotypic differences between individuals and between groups of similar individuals and groups of other similar individuals. But that really is the key, isn't it?

The question is not are there differences, but what difference are we focusing on AND powerfully WHY. Racist judgement oozes like a sore from the WHY part of this question. Scientific objectivism must identify both WHAT and WHY and use WHY to explain away racist judgement. How so?

Hierarchical assignment should not include a valuation such that it lends credibility to racist judgement. The existence of a hierarchy is not always objective as well, and is highly dependent upon the subjective determination of the value of a characteristic to an individual organism to survive, adapt, and excel within the context of its environment. And moreover, genetic evolution is not always a rapid response to such an environment - there is a lag involved and so current differences cannot be attributed to current conditions necessarily, nor can they explain mechanisms for now when they were derived then. Add to this the more rapid and disruptive mechanisms of genetic change from exogenous agents such as radiation and chance aberrations in genetic material transmissions. Clearly, racist dogma and rationalization cannot be supported by differences resulting from chaotic events.

This article is important in that it brings attention to critical issues in science that have been warped and distorted to serve political and putatively "moral" positions of persons or groups which end up hi-jacking scientific objectivism to support spurious and distorted racial judgements and agendas, but also to support religious dogmas and beliefs, often in ways far distorted from what the facts support and describe.

Unfortunately, the article does not stress the need for scientific objectivism enough and does not address how errors to judgement occur and can be identified by the press and public who may want to call to question the distorted claims of the judgmental, the intolerant, and fearful and hate-mongering amongst us.

To be of greater value, perhaps this author group might wish to address the issues of identifying the ill-spirited misuse of scientific knowledge to support harmful social judgements. Overall, a needed position statement in need of more detail and operational functionality.

Data "waves" in SNP array data

Kylie Louise Gorringe — 2008-07-01T00:00:00Z

We sometimes observe data "waves" in our Affy SNP array copy number data. It is inconsistent between samples or experimental batches and sometimes a second DNA prep or extra clean-up of the same sample removes the effect. It seems to be more common in whole-genome amplified DNA or DNA from limited sources (eg tumour biopsies). I'd be interested to know if anyone has identified why this occurs or has a solution for analysing tumor data.

fighting back against anti-science legislatures

Steven Salzberg — 2008-06-30T00:00:00Z

Greg, you make some excellent points - and I concur with your suggestion not to hold conferences in states that undermine the teaching of evolution.

Another strategy we might consider - those of us in academia, that is - is announcing that we will downgrade applications for admission to our universities from students in states where evolution is not taught, or is taught badly. The quality of a student's education is a legitimate criterion for admission to university, and if a state wants to damage its own students by teaching pseudoscience, then the citizens of that state should be told that they are hurting the chances of their children to be admitted to college. Maybe that would wake up enough parents to stop the legislatures from passing any more of these backward-looking, anti-science laws.

-Steven Salzberg

http://genefinding.blogspot.com

Why present-day Plantae have no chlamydial symbionts?

Cesar Sanchez — 2008-06-23T00:00:00Z

Excellent article. I very much enjoyed the detailed discussion of alternative hypotheses and phylogenies. I didn't know about the chlamydial role on plastid origin until I read a recent article confirming and expanding the results presented here:

Moustafa A, Reyes-Prieto A, Bhattacharya D (2008) Chlamydiae Has Contributed at Least 55 Genes to Plantae with Predominantly Plastid Functions. PLoS ONE 3(5): e2205. doi:10.1371/journal.pone.0002205

At the PLoS ONE site I have posted a comment/question (that of the title of the present comment), in case anybody can contribute to the discussion.

Correction

Caroline Hering — 2008-05-13T00:00:00Z

An incorrect FACS plot for CD44 expression of mClone-3 was inadvertently used in the final version of the paper. This has now been corrected.

Evidence for racial differences?

Peter Uetz — 2007-12-10T00:00:00Z

Petsko claims that "we have the data to refute the claims that one race is superior and another inferior or that gender is linked to intellectual fitness". Do we? Where is that data? On the contrary, I think there is evidence showing that some races are superior to others. Look at the 100 m Olympic finalists, they are pretty much all black. This is good evidence that black athletes are superior to white ones. Maybe there is a similar imbalance for academics. Same for sex. Men are undoubtedly much better at crime than women (aren't 90% of all inmates male?). Am I a racist? Hopefully not - I am even in a bi-racial relationship. But it is undeniable that there are differences between different populations. This is biology.

As long as these average differences are small (and they probably are) they have no predictive power for any individual and are thus useless. I see that these are very delicate issues and it may be risky to bring them up but there is no reason to avoid them. However, it shows that public opinion rather depends on emotion than on data.