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. :)

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

Microsoft makes good stuff?

I’m writing this post using Windows Live Writer which is actually a pretty nifty piece of software to blog with.

It neatly detected my blog (given just the URL) and with my username and password, it happily downloaded the theme from the blog, so that I get a preview of what my post will look like as I create it. Even WordPress doesn’t do that yet although that will change in WordPress 3.0 (at least for the new default theme.) Your blog will need to support XML-RPC or Atom publishing to do this kind of cool stuff though.

What’s also cool is that the interface is blog-agnostic. I could be using it to post to a Blogger blog, a WordPress blog, LiveJournal or TypePad, not to mention Microsoft’s own Live Spaces and Sharepoint blogs.

What I’d really love though is for there to be an add-on for Firefox or an extension for Chrome, so that I could quickly open Windows Live Writer after selecting an excerpt or an image on a web-page or link. If I was using Internet Explorer, I could use the Live toolbar to hook into Live Writer, but no way I’m using that browser or another toolbar. I like my vertical space! :)

P.S. Almost 4 years ago, I had blogged about a Firefox add-on called Performancing which did just that. Sadly, the Performancing add-on seems to have died soon after and the site itself is now some sort of blog consultancy service.

Doctor Who and The pH below

After two episodes, I’m quite enjoying the 11th Doctor. Matt Smith seems to be a bit of David Tennant clone, but I think he should soon have a persona of his own.

This week’s episode, “The Beast Below” takes place in the 29th century. I won’t say anything more, but apparently in 800 or so years, we’ll be going back to using analog pH meters!

Doctor Who - pH meter

The Doctor uses a pH meter to save the day!

Change

I had to do some shifting around with my hosting, so I thought I might as well make some long overdue changes too.

I got rid of the WordPressMU installation I was using. Of course with the upcoming 3.0 release of WordPress, that shouldn’t matter because they’re merging the codebases.

I merged the science and tech blogs that resided under a subdomain into this one. It meant I had to delete a couple of posts written by collaborators but that doesn’t matter since the whole collaboration experiment failed. I guess all of us were too busy to actually post here frequently.

The other big change I made was to move what used to be my anonymous personal blog that I’d been writing since 2003 into its own WordPress installation under a folder here. I had begun that blog on Blogger in August 2003 when I was still living in the US and back when Blogger didn’t have commenting! It was fun to go back and read some of my posts again, brought a few memories rushing back. I don’t plan to post there anymore, it’s now just an archive at http://absolutegeeky.com/oook

I’m still going to add a few more bells and whistles to this blog here and maybe I’d also post more often, I dunno. For now, the best place to find me usually is on Twitter or Facebook.

Refresh

I picked a new theme for the blog. It’s called Cleanr and mostly lives up to its name. I haven’t had the time to poke around or customise it, but maybe I’ll do that next weekend.

I suppose this might also make me post here more often? ;)

I’m back!

A significant proportion of my blog posts are of the “I’m back” variety. Well, maybe not on this blog… Not yet at least.

Anyway, it’s been a really really long time since I posted here and so much has changed in my life since then it’s crazy even trying to recap.

I did re-organize stuff and the posts that used to be under atheism.absolutegeeky.com have been added here. I might even just move to a single WordPress installation and roll all the posts into it. (I’m currently running WordPressMU)

So what prompted my return? Well, I recently looked into my hosting space because I was moving a friend’s site onto it and so logged into my blog. I found a zillion spam awaiting moderation and there was no “Delete All.” Sigh.

Anyway, that prompted me to make one more attempt to get this back on track. So collaborators or no on the Science and Tech blogs, I’m going to try and write here as regularly as I can.

Maybe I can do a recap…

Protected intolerance

I recently started reading this online comic called Cectic and while many a time the strip is bizarre or not so easy to understand, sometimes it’s crystal clear. Like the one below.

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?

Dual screen bliss

I usually carry my laptop to work and manage to do most of my work on that. But I still have a desktop machine which stores a lot of the data as well the two other work email addresses I have to manage (in addition to my own.)

Having to move my laptop out of the way and work on the desktop every now and then was getting to be a bit of a pain, so the first thing I did was install TightVNC on the desktop so that I can remotely access it from my laptop.

Once I did that, I realised that the LCD screen that came with my desktop would then be redundant. And then the light dawned. I could hook it up to my laptop as a secondary screen and extend my desktop onto it! Woo hoo!

Fifteen minutes later and a lot of digging around under the desk for cables and such, I now have a very nice dual screen and dual computer set up.

Hacking Vista

This is possibly just one of many ways you can get access to a computer running Vista. The crazy thing about this exploit is that all you require is a Live Linux CD that allows you to copy/rename files on an NTFS partition. There’s no dearth of those, the one used in the video is called Back Track

The steps are very, very simple; even your grandma could do it! All she’d have to do is watch this video and follow the same steps.

Scary? You bet!

Update: There’s quite a lot of discussion on Slashdot about this including people pointing out that a variant of this hack was available on Windows XP and 2000 too. But the more important point made was that if you have physical access to a computer and that computer’s hard disk is unencrypted (both of which are prerequisites for this hack) then you pretty much own the computer anyway. I guess the utility of this hack is for SysAdmins so that if they ever find themselves with a Vista box without a password, this is a useful way to get in.