Evolution of Your DNA: New Software Traces the Very Code of Life

There's a new computer program that knows all about your history - but don't worry, it's not going to report those parking violations or tell your friends what you do at night.  It cares about your real history - the evolution of your DNA.

Researchers at Penn State have created the impressively named Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST to its friends - and yes, the team who are tracing the very code of life did just jam in an extra letter to make the name cooler).  This software, when it's not hunting Doctor Who, can contrast and compare multiple protein sequences called 'retroelements'.  These biological building blocks have existed for a long time, and since they make up half of YOU and many other things (genome-wise) they're pretty useful signposts.

The program can trace the relationships between organisms as varied as bacteria and HIV, producing an tree detailing the evolutionary "distances" between each.  It compares every single pair of sequences, and without the subjectivity (not to mention boredom) of human experts performing the same task.  Also, the program can operate in the less-than-25%-similar 'twilight zone' where other programs fear to tread.

Even better, these scientists are making the whole thing open-source - so that anyone who wants can trace phylogenetic pathways in their spare time (assuming they have access to a few million dollars of genetics laboratory).  Okay, maybe it isn't the sort of thing you'll see people swiping into their iPhones (until society gets good and GATTACA'd up), but the concept of spending years on an amazing program, then just making it free because it's useful, is a great one.

The researchers also report that the program is learning rapidly as it acquires new data, and has already evolved considerably since they first activated it.  But we're sure there's no danger in an evolutionary-minded, open-source and web-wide program that can do that.

Posted by Luke McKinney.

Evolutionary Distance Measurement

Official Paper (pdf) 

Comments

[erichansa]

The program can trace the relationships between organisms as varied as bacteria and HIV, producing an tree detailing the evolutionary "distances" between each.
that's cool

[Jiff Weeder]

Dude that is quite fascinating indeed. Those scientists dudes are pretty smart.

Jiff
www.anonymize.us.tc

[Chad]

If this software can measure the genetic differences between organisms in the same lineage and measure the evolutionary distance, does that mean it could also predict the next evolutionary change?

[Scott Fanetti]

Chad,

Evolution does not work like that. It has no sense of future change. Random changes occur in populations that are under selective pressure. The changes that have a neutral or positive effect on the reproductive rate of a population tend to increase in frequency within a population over time.

This means that if a founders exists in a population that has a certain mutation, and that mutation gives it a 30% greater chance of bearing and raising children, he will have 4 children for every 3 children his neighbor has. The children with the beneficial mutation will all have 1 more child than their neighbors without the mutation. Over time, the number of members of the population with the mutation will dwarf the number of members without it. These changes accumulate over time and lead to the wide varieties of life forms we see today.

Humans have not really been under selective pressure for the past hundred years or so. But we are in the position now to guide our offspring's genetic futures. This is not really new since humans have been artificially selecting randomly varied organisms for thousands of years - we just call that agriculture.

Corn for example was engineered by humans who selected the best ears for reproduction over generations. The aztec farmers took a weed with tiny hard seeds and relied on non random selection of random mutations to turn that into the corn we see today. All the food you see in supermarkets is a result of this same process.

People freak out about genetically engineered foods - but they don't seem to realize humans have been doing this for hundreds of generations. Its just now, we know what we are doing.

[Rob]

I think BLAST is "Basic Local Alignment *Search* Tool", you'll be glad to know that they didn't just chuck in the S for the coolness alone :)
http://en.wikipedia.org/wiki/BLAST

[Charlie]

Darwin said the primary force behind evolution of humans is sexual selection. This appears to be true in practice (and is a cause for concern when modern medicine allows manipulation of fertility and pheromone production) but in the long run our species will evolve or perish regardless of our individual actions; the activities of the group/society are changing the global environment in ways that will force adaptation or extinction. You need to join with a group, or take control of a group, in order to have significant effect on future evolution.

[Marlon]

And as far as your "GATTACA'd up" comment goes. We've been doing that for years as well - though perhaps in the other direction - with in vitro fertilization.

Helping people - who either don't 'match' naturally or due to medical disposition - have kids by 'forging' a bunch embryos only to subsequently select the 'strongest' of the bunch.

Though laced in ethical debate as to whether it is a "god" given right for anybody to bear children by any means or not, this is by definition, a selection of a living life form based on its genetics. Though more for survivability rather than superiority.

The actual genetic engineering of changing an eye-color, or bettering the immune system is just a step away.

Where people you can't have children, because they don't 'match' naturally or due to medical condition, are given a 'helping hand' in creating a bunch of embryos only to subsequently select the "strongest".

[Alkhemist]

Evolution has recently been shown to happen in "quantum jumps," and there is no way to predict when or how this will happen in a given species.

As to GM foods -- yes, we "we know what we are doing" now, but the problem is HOW these foods are being modified. When seeds are created to not be able to reproduce (and they are), it puts those with the seeds in power and those who need them become dependent on those who have the seeds. This is already happening in poor countries, and is quite evil, IMO.

[Sexy Pinay]

very interesting article! thanks for this!

[EvilCosmicMonkey from Knoxville]

Could this help to select genetic traits to improve the human race - like maybe splicing out the gene for diabetes, colon or lung cancer, or Alzheimer's ?

If GDDA - BLAST was capable of doing that, it would be quite the double - edged sword.

[Rob]

@EvilCosmicMonkey

The program can't modify any genetic modification, it's not really about genetic modification at all. It's about making phylogenetic trees - giant family trees for showing how related different species are. You give it a bunch of files that contain genetic sequences for different species, and it looks at how similar those sequences are. Based on the levels of similarity, the program will construct a tree that estimates when one species became two.

[Rob]

Correction:
modify any genetic *information*
Sorry, my bad.

[EvilCosmicMonkey from Knoxville]

Rob -

I think I meant " Could it help in genetic modification " by making such phylogenetic trees / maps ?

There seems to be a distrust of any technology involving DNA. ( The " Playing God " angle ).