Sequence is not everything

by mira66

IBM’s “DNA Transistor” Could Sequence Genomes on the Cheap
[Via Discover Magazine ]

When the Human Genome Project finished sequencing the first human genome earlier this decade, the price tag for the endeavor had reached almost $3 billion. Now, IBM has announced details of its effort to bring the cost of sequencing a person’s genome down to below $1,000–and the company says it could go as low as $100. While IBM is hardly the only company racing towards these goals, the company’s chip-based approach makes it a serious contender.

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The discussion of course leads into the worries that knowing the DNA sequence determines a person’s entire life. So if the insurance companies know what your genetic background is, they will know what diseases you are going to get, etc.

This displays a very simplistic view of how our bodies work. There are many other factors that have an impact on many complex diseases that will greatly complicate the picture. Simply knowing the sequence will not be enough.

This can easily be seen by the fact that every cell in the body has the same genetic sequence but there are a huge variety of cells. They are all formed by differential expression of the genetic sequence.

Genes very seldom do anything by themselves. It is the RNA molecules that produce the proteins that do things. Sometimes the RNA itself is responsible for an effect. These products can have altered expression levels that influence the body. They can also have very different forms, depending on the circumstances.

In addition, there are continuing discovery of epigentic factors that control the expression of genes and their products. Methylation is one instance. Alternative splicing is another. I have written about the possibility that modified histones (which act as structural anchors for the genetic material) could have an effect on the entire process of gene expression.

Some of these epigenetic effects can be inherited., increasing the complexity of the matter.

Knowing someone’s genomic sequence is a helpful tool and can be used to help understand some thing but we are much more complex than a string of letters and this complexity may well be revealed when we actually get a process for $100 sequences.

(Of course, that result had better be very, very accurate. There are 3 billion bases in the human genome and even an error rate of 1 in 10,000 would mean that there would be 300,000 errors. This could have substantial ramifications if the error is in a vital gene.)

I tend to think that a major area where $100 genomes will be used will be to actually sequence the expressed RNAs in particular cells. It is relatively easy to convert the RNA to DNA for sequencing. Being able to then get a handle on the exact sequences being used in specific cells, and their amounts, would be very useful indeed.

Where is Roddy McDowall when we need him?

by Howdy, I’m H. Michael Karshis

‘This Country Is Going To The Apes’ … Lovely
[Via Sadly, No!]

Here’s Paul A. Ibbetson, ‘lecturer on the Patriot Act’:

A return to the Planet of the Apes

By Paul A. Ibbetson

… Before I begin to share why I believe this country is going to the apes (self-deserved destruction), which I am sure will make the fur fly among many who would falsely infer my assessment is focused somehow on race, instead of policy, and accuse me of crossing into the forbidden zone, let’s look at the overall message that the Planet of the Apes movies tried to convey.

Yes, let’s, Mr. Ibbetson. Lest our ape fur fly at the silly suggestion that your column comparing Barack Obama’s America to the Planet of the Apes might somehow be about race.

Take but a moment to look around you and it won’t take long to see the deadly preparation for chaos that is unfolding from every corner of this country.

It’s like the anarchist boy scout said, ‘Be prepared … for chaos!’

The United States has elected a president in Barack Obama, who when not busy fomenting racial conflict among the people who voted him into the most powerful position in the world, works with every ounce of his strength to destabilize the traditional pillars of this country.

Damn that talking ape Obama for fomenting racial conflict! And even worse, using his ape-like sinews to destabilize the tradition of comparing black people to apes!

This same president invites the apocalypse worthy of the Ape World by emasculating the United States through ill conceived military weakness in foreign assemblies, such as the United Nations.

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Many people have remarked on the “overall message that the Planet of the Apes movies tried to convey”: it was a movie about race relations. The book, Planet of the Apes as American Myth: Race, Politics, and Popular Culture, author Eric Greene discusses exactly this. He mentions that Sammy Davis Jr. told the producers that he thought it was best movie on black-white relations he had seen.

The ape insurrection in Conquest of the Planet of the Apes was based on the Watts riots, according to the screenwriter. In fact, Conquest discusses race relations in much more overt style than the other movies but the underlying motifs of bigotry and persecution is present in all of them.

For anyone to suggest that the Apes series does not focus on race is to reveal a strong lack of history and context. To try and claim that comparing Obama to the Ape leaders has nothing to do with race is to be supremely blinkered when it comes to any sort of examination.

The purpose of writing such an article should be to see how the movies help inform us about life some 40 years after they were made. But the bomb that was worshipped in Beneath the Planet of the Apes had nothing to do with Iran and everything to do with the Cold War and the continuing militarization. I do not think community aacitivists from ACORN ever appear in the movies.

I hate it when movies are shoehorned into someone’s preconceived notion, one that seems to have so few reflective aspects. Planet of the Apes has so many awesome parts but one of them was the obvious role reversal between Caucasians, who go from the top of society to the bottom. Even the minority audiences recognized this and cheered on the apes in later movies.

If this was a term paper, I’d give it a C. A potentially unique view provided only haphazard factual support with little connection to what was up on the screen. Horrible metaphors – … “caught up in the nets of our own demise” (what does that even mean?) mixed in with Junior High school sophistry – “This same president invites the apocalypse worthy of the Ape World by emasculating the United States through ill conceived military weakness in foreign assemblies, such as the United Nations.” That just does not even make much sense.

Look we get that the thing about these movies that is most upsetting to the author is that the white guys are not in charge (It’s run by those ‘damned, dirty apes’). Yet anyone who sees his writing as being based on any sort of racism is making a false inference? Right!

Well, when you chose a movie series that has subtexts directly dealing with racial relations, where overt actions mimic contemporary evens, such as race riots, and that demonstrates again and again the dehumanizing aspects of bigotry and prejudice, but you refuse to see anything racial about the series, I would have to suggest that the author may not have actually seen the movies. Perhaps Conservapedia is working on its own version of the movie, like it is working on its own version of the Bible.

So instead of saying “Get your stinking paws off me, you damned dirty ape”, Heston says “Curse you for emasculating my military in foreign assemblies.”

Or maybe this – “You Maniacs! You blew it up! Ah, damn you! God damn you all to hell!” – would become this – “You Maniacs! You elected a President who when not busy fomenting racial conflict among the people who voted him into the most powerful position in the world, works with every ounce of his strength to destabilize the traditional pillars of this country! Ah, darn you! Gosh darn you all to heck!”

I think Charlton might kick somebody’s ass if this were true.