When we were in school, we had to study both English prose and poetry. I found the poetry part quite boring, as I could not really understand any of it. Some people, I guess, get so engrossed in making things rhyme that they lose track of what the heck they were trying to say. That was my opinion of most poetry. The only guy I kind of liked at the time was Ogden Nash. But wait a minute, a quick search in google reveals that "am I a child or an adult" was actually written by Margaret Lawrence. OK, forget everything I said about Ogden Nash. BTW, Margaret Lawrence apparently wrote that poem when she started an illicit affair with her teacher at the age of 14. Some people have all the fun in the world. Forget about that too, because this post is all about science, thats right, fooled you didnt I ? Or maybe I harmed my own blog by twisting my own arguments, hmmm needs some thinking...
Anyways, the actual content of the post is not so much the poem, but the confusion that arises when you are at the cusp of two different things. Most importantly when there is a continuum between two different things such as childhood and adulthood. Until now, I am sure most of you have this concept that there are two kinds of organisms (actually three kinds), one is a prokaryote and the other is a eukaryote (third one being archea). You might recall that the two have quite distinct cell morphology, with eukaryotes having membrane bound organelles, which bacteria completely lack. And also the ribosomal RNA is different in the two. Not to mention the complex signaling that has evolved in eukaryotes as compared to bacteria. Now, I will first challenge the second opinion. What I did was plot the variation in length of 16s rRNA from all 180,000 or so organisms in RDB (Ribosomal DataBase). I filtered all 16S rRNA's less than 1200 as this is the cutoff the RDB suggests is a good criteria to filter out spurious hits. So, I was left with around 130,000 rRNAs isloated from multiple organisms (including multiple strains and clinical isolates). The distribution is given below.
I cant be bothered to make it nice etc, but the X-axis is the length of rRNA and the y-axis the frequency of observing the said rRNA length. The average length in bacteria is around 1500 nucleotides (E.coli 16S rRNA length). The value for eukaryotes is around 1900, which gives the eukaryotes an 18S rRNA.Two things jump out at me. One, the very long tail that almost goes as far as 2600 nt. Now, if you believe the long tail is real, then it means that some bacteria have very long rRNAs, even longer than eukaryotes. So, we see a continuum in rRNA length. Even if you dont think it is real, look at the shape of the curve. I perceive a left skew. Now, most of these rRNAs are found by using universal primers at the ends of rRNAs. Due to rRNA transcription, the beginning needs to be somewhat similar in all organisms. But what about the end ? For example, what if the real distribution is a normal distribution, but we are artificially cutting it at the right end ? We would get shorter-than-they-really-are rRNAs, explaining the skewed distribution. In other words, even if you remove the long tail as spurious, there is still some doubt left on the continuity of the rRNA length between prokaryotes and eukaryotes. I need to align them and see what happens. That is left for another project.
Now, coming back to the original points, prokrayotes do not have membrane bound organelles, right ? Dead wrong. It seems there is an entire class of bacteria, the Planctomycetes which have membrane bound nucleus, complete with all the pores and protrusions. Read about it here (http://www.nature.com/scitable/topicpage/beyond-prokaryotes-and-eukaryotes-planctomycetes-and-cell-14158971). So, another shibboleth of discontinuity of bacteria and eukaryotes demolished. What is left ? The complex signaling you say ? Bacteria dont have protein kinases, is that what I hear ? Ta-ta-da, Dead wrong again. Here's the plot giving average genome sizes (red color) and the number of protein kinases (green color) in each class:
You see the big shiny green bar around Planctomycetia ? You cant miss it, its one of the biggest. So, there you go, all three shibboleths of discontinuity of prokaryotes and eukaroytes blown away. Its like what Leaky told Jane Goodall :
"Now we must redefine ‘tool,’ redefine ‘man’ or accept chimpanzees as humans."
So, either we must redefine er...Planctomycetia (?) redefine prokaryotes, or accept that Planctomycetia are eukaryotes. BTW, in case you dunderheads have not figured it out, the "am I a child or an adult" allegorically points to the confusion that Planctomycetia have about whether they are prokrayotes or eukaryotes. And it is my way of telling you people, that just like there is no clear demarcation between the two stages, so is it with the (pro/eu)karyotes. Just kidding, I know you got that long time ago...
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