Category Archives: Biology

Life with a synthetic genome

If you haven’t already seen this plastered all over the news, Craig Venter’s team has created the first replicating cell using a completely synthetic genome.

The video of the press conference while a bit dry, is definitely worth watching

I haven’t read the paper yet, so this is a quick summary based on the conference and on reports elsewhere.

First to clear things up, this is not a completely synthetic life-form. Only the DNA of the life was synthesized outside of a cell and then assembled and inserted into a host cell (of another species.) The DNA was made of known sequences with a few added “watermarks” as Venter says. Even so, this is a remarkable accomplishment and if nothing else demonstrates that there is no special “vital force” in DNA that causes life.

What’s even more exciting about this is the technological breakthroughs the team had to make and the insights into what is necessary for life. For instance the number of genes that were “disposable” in an already minimalistic genome, the ability to grow the synthetic genome in a yeast cell, extracting it from there and then transplanting it into the host cell.

The “watermarks” are an interesting feature too. As I’ve gathered from the video, they’ve added the names of the scientists involved as well as 3 quotations in the genome. These messages are themselves encoded (as a kind of puzzle, I suppose.) Also, to make sure this added code doesn’t form proteins, another layer of encoding is used to insert stop codons. As Venter says, “a code within a code within a code.”

The funny thing though is that this code won’t last long if they continue to grow the bacterium naturally. Since the code by design has to be in non-coding “junk” DNA, it’s not going to be conserved evolutionarily. Point mutations will accumulate over time and since the organism has been designed to have a short life span, the code is bound to be garbled quite soon, maybe even before someone has time to break it. ­čÖé

I should have another post once I’ve grokked the paper and read some more of the commentary online.

One small step for a bacterium…

…one giant leap backwards for man.

A recent paper out of Richard Lenski‘s lab at MSU details the evolution of a Cit+ strain of E. coli among the 12 replicate lines that are part of the Long Term Experiment in Evolution running in his lab

I haven’t read the paper yet, but from the abstract, it seems the evolution of a relatively radical new trait (for E. coli) which is the utilisation of citrate as a carbon source has been demonstrated and also it is shown that this trait was contingent on the “history” of that particular line that developed the trait. Essentially, the other 11 lines did not gain the ability to use citrate even on subsequent experiments with earlier generations, but the line that did evolve could do so again and again from earlier generations that didn’t have the ability.

Understandably, this is an important study in evolution for the role of historical contingency (read “chance”) but also in demonstrating that an ability (or lack of) that partially defined the species in question had evolved in the lab.

But more on that in another blogpost.

What has struck me about the news surrounding this paper on the net has been the vigour with which the results, the science (and sometimes even the scientists) are been questioned and attacked by what I can only charitably call the “god” brigade.

Part of the reason could possibly be because of the way the New Scientist article about the paper ends:

Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”

That one short paragraph seems to have got their collective goat and has led to a flood of comments on the New Scientist site. The giant leap backwards is that a lot of the people commenting seem rational, coherent and somewhat aware of the biology but somehow perversely blind to the idea of evolution.

The old chestnuts about micro-evolution and macro-evolution are trotted out numerous times as well as variants of “But it’s still a bacterium” not to mention “It’s all random therefore we are random.”

A quick sampling of some of the inane comments:

Back on topic, i’m a more logical guy so I think things through. There’s no black and white, noobs.

Anyway, personally, it seems to me the mutation at generation 20,000 could be evolution (however, evolution refers to advantage, and until this scientist figures out what REALLY happened, we don’t know if that change was technically advantageous or disadvantageous. I think we can assume advantages since they survived. Survival of the fittest, right?)

However, I see this article fails to mention epigenetics!! Epigenetics very well could be the CAUSE of the WHOLE series of changes, OR, there was a random mutation first (evolution), which made it easier for epigenetics to take over, causing the Cit+ trait.

Sigh. Where do you begin with comments like that?

On the other hand if the basis of evolution is randomness, then that destroys the entire foundation that science is built upon. The evolution to human beings is also random. What we see and think are also therefore random. All our theories are therefore random. We cannot really be sure whether we have really evolved or not, if we base evolution on randomness, since everything is random. We cannot even be sure that we are thinking, after all it might be just some random hallucination. We cannot be sure of anything. One cannot build a rational world on disorder.

Oh wow.

This article doesn’t explain why this is a a major innovation.

A flagellum would be major.

I suppose if someone WERE to demonstrate the evolution of a flagellum it would be dismissed as not major. Like clockwork, the next comment states:

Even a flagellum would not be major. If evolution is responsible for all biological structures — and that is a BIG IF — then the human brain, which is capable of advanced mathematics, language, and philosophy, is evolution’s greatest triumph.

And to end:

What Bothers Me Most Is that the evolutionary biologist at UC has already formed a conclusion before the initial research has been completed and published. This doesn’t seem very scientific of him, or the article for quoting him. I kind of get the impression that New Scientist has a chip on it’s shoulder when it comes to creationist. There are loads of “theories” out there on a milieu of topics, which aren’t accepted by the scientific community at large (creationism obviously falls into this category), yet NS seems to single creationism out for needing repeated condescension…

I guess 20 years of experiments and published papers don’t count for squat?

But, but… Mom said…

The dentist from our┬áTee Family Dental┬ádecided to look through past research papers to see if I needed any more work on done my teeth, since I’ve being doing a lot of oil pulling lately and you might ask what is oil pulling?T Well this is the practice of swirling oil around your mouth and then spitting it out. It usually involves coconut oil, sunflower oil or sesame seed oil. Rinsing should be continued for perhaps 5 to 20 minutes, so that the edible oil is pulled through the teeth and mouth.

Various websites advocate coconut oil pulling as an effective way to whiten teeth and remove bacteria. Some advocates online suggest it can treat tooth decay, kill bad breath, heal bleeding gums, prevent cavities and even prevent heart disease. There is a book, entitled Oil pulling therapy,1 that promises it exerts a powerful cleansing and healing effect on the mouth and sinuses and the rest of the body.

Their research was published this week in the British Medical Journal, and the Guardian has a story about them here.

What can I say? I told you so, Ma! ­čÖé

The Inner Life of a Cell

For all biologists who couldn’t think in 3-D, and were bored of illustrations in text books. This will really show you how dynamic life is, even at the level of a single cell.

http://www.youtube.com/watch?v=MMrvmZ2i1sE

David Bolinsky, former lead medical illustrator at Yale, lead animator John Leibler, and Mike Astrachan are some of the creators at XIVIO who made the movie. They created the animation for Harvard’s Department of Molecular and Cellular Biology. Most of the processes animated were the result of Alain Viel’s Ph.D. work describing the processes to the team.

14 months to create for 8.5 minutes of animation! Well worth it, don’t you think?

For more on how it was made, read Studio Daily’s report here. And an interview with Wired here.

(posted originally by MadGenius)

The State of Evolution

Kansas Evolution

From the cartoons of R J Matson

Hello World!!

High time I did post here, before more people start doubting my very existence. Had planned initially to blog on something else, but that didn’t happen. That’s a long story, and I will not repeat it here.

As this is going to be an introductory post, I think I shall tell you about what I do. I work in a small bioinformatics based company in my hometown as a research associate. That’s my designation, although I don’t really do any research. What I do is ‘literature curation’ – a field which not many people in biology actually know off. What it involves is basically reading research papers, putting all that data together, and help improve biological databases. Once the data has been collated and meaningfully put together, it can be then used for finding drug targets, designing experiements, etc etc. This ‘collation’ of data can range from simple keyword/abstract indexing of papers to building signalling pathways in specific cell systems.

For more, have a look at these articles from PLoS Computational Biology. Last month’s issue had a very nice editorial on the role of ‘Biocurators’. I especially loved this-

Biocurators can be considered the museum catalogers of the Internet age: they turn inert and unidentifiable objects (now virtual) into a powerful exhibit from which we can all marvel and learn. That would be a decent enough contribution to the world of science, but the task of the biocurator is even more extensive. Computational biologists do not expect to merely walk through the door, cast a casual eye over the exhibit, and exit wiser (although we frequently do); we also want to add our own data to the exhibit, plus pick and choose pieces of it to take home and create new exhibits of our own. Oh, and we would like to do all these things with minimal effort, please. We can be a pretty exacting bunch of customers, and it takes skills over and above a knowledge of biology to juggle the different needs of data submitters, information seekers, and power players.

This wonderful article gives a comprehensive description of a curator’s job while dealing with a (slightly) static database, while this one describes how data can be put together to create a (more dynamic) interaction database.

(originally posted by MadGenius)