Monthly Archives: July 2009

Revelation

Group Think

From Researcher Condemns Conformity Among His Peers:

Journalists, of course, are conformists too. So are most other professions. There’s a powerful human urge to belong inside the group, to think like the majority, to lick the boss’s shoes, and to win the group’s approval by trashing dissenters.

The strength of this urge to conform can silence even those who have good reason to think the majority is wrong. You’re an expert because all your peers recognize you as such. But if you start to get too far out of line with what your peers believe, they will look at you askance and start to withdraw the informal title of “expert” they have implicitly bestowed on you. Then you’ll bear the less comfortable label of “maverick,” which is only a few stops short of “scapegoat” or “pariah.”

and

Conformity and group-think are attitudes of particular danger in science, an endeavor that is inherently revolutionary because progress often depends on overturning established wisdom. It’s obvious that least 100 genes must be needed to convert a human or animal cell back to its embryonic state. Or at least it was obvious to almost everyone until Shinya Yamanaka of Kyoto University showed it could be done with just 4.

The academic monocultures referred to by Dr. Bouchard are the kind of thing that sabotages scientific creativity.

Using the Ribosome to Encode a Brain Protein

Let me explain some more about the human brain protein that is encoded by the ribosomal S5 protein.

As most of you probably know, DNA is a double-stranded chain of nucleotides.  When it is time to express a gene, the RNA polymerase unwinds the DNA and uses only one of the strands to make a copy in the RNA format as shown in the figure below:

What I showed with S5 is that while the bottom strand codes for this highly conserved ribosomal protein, the upper complementary strand, if it were to be transcribed and translated, would code for an unnamed protein product isolated from the human brain.

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Digging Up More Buried Code with Ribosomal Protein S5

We have been focused on the ribosome as one plausible vehicle for front-loading evolution.  This hypothesis led us to successfully expect ribosomal proteins would carry out additional functions and that some portions of the ribosomal RNA might actually code for protein.  So it’s time to dig a little deeper.

I recently noted that the small ribosomal subunit protein, S5, also moonlights in the differentiation of red blood cells.  One thing that is striking about S5 is its highly conserved amino acid sequence.

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Evil Planz

Buried Code

We have already seen that most of the universal small subunit ribosomal proteins have alternative functions. If ribosomal proteins can be used as a vehicle for front-loading, given that a designer can count on the ribosome being perpetuated far into the future with minimal changes, why not also use the ribosomal RNA (rRNA) itself?

rRNA forms the functional part of the ribosome where, with the help of the ribosomal proteins, it folds into a complex 3D structure that interacts with the messenger RNA (mRNA) and transfer RNAs to carry out the core processes of protein synthesis. While rRNA, which is synthesized by RNA polymerase 1 is typically the end-product, natural genetic engineering processes could copy and transplant rRNA sequence so that it was under the control of an RNA polymerase II promoter. This would mean that the rRNA sequence would suddenly find itself being transcribed as mRNA and thus translated into a protein.

A clever front-loader might encode proteins-for-the-future in the rRNA sequence itself. In other words, while rRNA sequence is not normally used to code for proteins, it could be used to store code for some proteins. Of course, the coding potential is limited, as rRNA sequence plays a crucial, conserved role in the process of protein synthesis. The ability to code amino acid sequence would thus be limited by the sequence needed for the rRNA to carry out its function. Nevertheless, the opportunity for some degree of front-loading exists.

With this in mind, I decided to take a rather unique approach and search for protein sequence encoded in rRNA. Continue reading

Another Ribosomal Protein Moonlights

The logic of front-loading allowed me to hypothesize that ribosomal proteins would moonlight. Admittedly, it is more like an expectation than a precise prediction, but what matters is that the hypothesis directed my attention with subsequent payoff. After determining that about 2/3 of the universal SSU ribosomal proteins appear to moonlight, the criterion of Rationality kicks in. That is, if it is possible to front-load alternative functions into ribosomal proteins, a good designer would attempt to maximally exploit this particular vehicle for front-loading. So if the ribosome was front-loaded where two out of three ribosomal proteins were preadapted, why not all of them? Using this logic, I then noted we should expect to find moonlighting roles for the other third of the universal SSU ribosomal proteins – s17, s5, s8, s11, and s15 – for which I could not find a potential moonlighting function.

So after writing up my original blog entry on moonlighting ribosomal proteins, I went back to the data bases to search more closely.

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