Nov
29
2009

Synthetic biology

Synthetic biology pioneer, Andrew Hessel, explains how building blocks of DNA snippets will be assembled into customized living organisms

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Medicine without patents

Andrew Hessel hopes that an open source approach in pharmacology will produce safe, effective, and individually personalized medicines quickly and inexpensively. Hessel likens the exponential advances in synthetic biology to the boom in the electronics industry.

Test tube sized factories

One big difference, though, is that biological manufacuring does not require expensive refining, huge factories, or expensive tools. Biological organisms are alive and can self assemble complex structures from basic ingredients.

Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells.

  • Cells are being engineered to consume agricultural products and produce liquid fuels.
  • Bacteria and yeast can be re-engineered for the low cost production of drugs. (Artemisinin, Lipitor)
  • Bacteria and T-cells can be rewired to circulate in the body and identify and treat diseased cells and tissues. BioBricks.org

DIY BIO 4 Beginners

Eric Fernandez has a blog for do-it-yourself types like 23-year-old Kay Aull who set up a do it yourself DNA lab for genotyping her GFE gene in her closet! Be sure to check the archives for more than a hundred informative DIY Bio posts like this one by Make's, Mac Cowell.

Gene hacking and biofabs

Costs are coming down fast and genetic synthesis or gene fabrication is a cottage industry. Biofabs like GeneArt, Blue Heron, DNA2.0, and Codon Devices can deliver a synthesized product from an e-mailed description almost over night. Synthetic biologists envision writing the DNA code for such products the way computer programmers write software.

Catolog for genetic parts

Genetic programming now has several well developed languages allowing large data bases of biological modules.

The Registry of Standard Biological Parts is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer. It provides a resource of available genetic parts to iGEM teams and academic labs.

iGEM synthetic biology contest for students

The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate Synthetic Biology competition. Teams participating and over 1200 participants will all specify, design, build, and test simple biological systems made from standard, interchangeable biological parts. If you go to this iGEM results page you will find video links for the winning presentations. You can read team abstracts of the iGEM projects here.

Your Comments, Thoughts, Questions, Ideas

ARTiFactor's picture
ARTiFactor says:

If you do not watch the whole video, be sure to watch from 15 minutes till about 30 minutes.

posted on Sun, 11/29/2009 - 4:52pm
ARTiFactor's picture
ARTiFactor says:

I recommend viewing this 46 pg PDF by Hessel explaining the iGEM program.

posted on Sun, 11/29/2009 - 4:56pm
Menno Mafait's picture

It's all nonsense!

1) As a bio-scientist Andrew should know that proteins consists of at least 300, but more likely over 1.000 amino acids, which exists in 20 'letters'. So, there are at least 20 to the power of 300 useless combinations for only 1 useful combination to form even the simplest kind of protein, but more likely: 1 : 20^1000 (a number with 1.000 digits !!!). Compare: The chance to win a big lottery can be written in only 8 digits and the numbers of atoms in the universe in 80 digits.

I call it "the humor of God" to build in such an 'idiot' amount of useless combinations (or such a high level of sophistication, if you like), that it would have taken - not billions - but zillions of years to form by chance.

But that's only to form ONE kind of protein. Life needs many kinds of proteins to be formed at the same spot, at the same time. I guess: One chance in a ZILLION TIMES ZILLION years.

No chance the evolution started like that!

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2) As a bio-scientist Andrew should know - or will discover soon by practicing Synthetic biology - that the concept of genes (DNA) is simply to rigid (or stable, if you like) for species to be evolved. Genes can not - and will never - accept new functions or a higher form of intelligence.

Proteins are super-super-super-sophisticated mechanisms (remember the huge numbers) and they only work together with a matching gene.

There are 3 categories of genes:
- Neutral genes, not essential for survival: Defects in those genes will cause for example: blond hair, white skin and blue eyes;
- Tolerant genes. Defects in those category of genes will cause an handicap (disease) in that organism. Although that organism will probably be weakened - it can survive;
- Essential genes. Any defect in one of those genes and that organism will inevitably die.

There is simply no chance evolution can BEAT the stability of the genes to form new species!

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3) As a bio-scientist Andrew should know there is no proof for those millions of years between the species. It is simply a concatenation of reasoning - ignoring debilitating facts.

The Carbon-14 dating method is can "determine the age of carbonaceous materials up to about 60,000 years old". (Wikipedia).

All other methods are based on the evolution theory itself. So, they can not be used to proof evolution!

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4) As a bio-scientist Andrew should know genes (DNA) only degenerates and can not increase in complexity.

Example: The Koala bear have lost it's ability to have a varied diet. Nowadays it only can accept eucalyptus leaves as food, which weakens this animal even more. They are doomed to distinguish.

No proof for any increasing complexity - only for DEGENERATION of genes (DNA) - which disproves evolution!

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5) According Andrew - as an evolutionist - some flowers decided during evolution to be completely dependent of the bee for their reproduction. A little problem: The bee was not invented yet. Please survive a few hundred million years without offspring...

(And if those flowers were evolved at the time the bee flew around: Why did those flowers gave up their successful reproduction method for an uncertain future together with the little bee? That would argue against evolution.)

No change for survival during those millions or billions of years the evolution should have taken!

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The irony of it all: The evolution theory is invalidated by SCIENTIFIC prove. And guess who is using this invalidated theory...

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About Synthetic biology: Why didn't Andrew show a very simple example? Was it all philosophy? An hype?

It's 2010 now. The Darwin year is over. I guess - also all Darwin-hypes are over: Genetic Programming, Synthetic biology, etc.

Soon the Higgs particle will be found. Let's create a hype about: Boson Biology!

posted on Tue, 01/05/2010 - 4:38pm
Steven's picture
Steven says:

In regards to:

1) I'm not totally sure what you're talking about. But, even if you've got your organic chemistry right, that's not how probability works.

"One chance in a ZILLION TIMES ZILLION years. No chance the evolution started like that!"

Those are, of course, absolutely contradictory statements. An incredibly small chance is still a chance, and given an incredible amount of time, it will happen. And, while we're at it, what are the odds of a supernatural being doing the job? Maybe great! Maybe nonexistent. There's no way to tell.

2) I don't think genes are tidily organized into three categories like that. You're assuming that all mutations must be categorized as neutral, sort of bad, and completely bad. Why? Why would that be the case? Even the examples you've given don't work for your argument. Skin tone, governed by a "neutral gene," can indeed affect an organism's success (i.e., its chance of surviving/reproducing) depending on the environmental pressures. Darker skin can protect a body from frequencies of solar radiation that can increase the chances of cancer. Lighter skin can allow a body to process more vitamin D in higher latitudes with less direct sunlight. Or consider your "tolerant" genes—let's consider mutations that cause conditions like sickle cell anemia or hemochromatosis. As you say, they can weaken an organism, if it survives at all. So why have they persisted? The genetic variation that causes sickle cell anemia is more prevalent in areas of the world where the environment is suitable for the transmission of malaria. Turns out that people with sickle cell genes are more resistant to malaria. So the environment selected for the gene. Oh, snap! Or hemochromatosis—a genetic mutation that causes a body to store too much iron, which can kill them. Except that mutation can be selected for in times when iron-rich food is scarce, meaning that it can also save the carrier's life. Say what?!

But, yeah, generally mutations kill you or do nothing. It would take practically forever for the rare beneficial mutations to accumulate enough to make a difference. Which brings us to...

3) We, as species, as life, do have practically forever. Yep, carbon dating is only reliable up to a point, but, fortunately we don't have to rely solely on carbon dating or "other methods based on evolutionary theory." We can examine stratigraphy, or we can use other forms of radiometric dating. Carbon dating is limited by carbon's relatively short half-life, but there are other elements with much longer periods of decay that we can use. And if they were deposited in the ground by something like a volcanic eruption, we have a definite starting point from which to measure. If we're using wikipedia, here. Take a look.

4) Where are you getting that? Genes only degenerate? Lots of species specialize, but that's definitely not the same thing as degeneration. You ought to try eating only eucalyptus. If, by some chance, it doesn't work out, do you think that's because humans too have degenerated past the point where we could use eucalyptus as food, or because we haven't evolved to take advantage of a food source that most species can't use? If eucalyptus trees went extinct, the koala might follow suit. But if other trees—but not the eucalyptus—went extinct, koalas would be just fine, and lots of other species would go extinct. So is that because they are genetically degenerated?

5) Do all pollinating plants rely entirely on bees? No. So it seems possible that flowers evolved without bees, but when those remarkable flying insects came along, they could have evolved with each other, each benefiting from the other's adaptations. Organisms don't adapt on the certainty of the future—we don't know the future, nor do non-sentient flowers—they adapt based on what works well over a long period of time. And flowers have had a long period of time, and evolving alongside bees has worked very well. Will it work well forever? Almost certainly not, but that's what happens. Another strategy will evolve, or species relying on the unsuccessful old adaptation will go extinct. It happens.

I think it's the opposite of ironic, really. What you would expect from the theory of evolution is what seems to be happening all around us. Not ironic.

(I'm excited about the Higgs Boson too!!)

posted on Tue, 01/05/2010 - 11:31pm
ARTiFactor's picture
ARTiFactor says:

One thing about science is that accepted theories change when new evidence requires it.
Which came first, flowers or bees?
Learn more by reading this. New York Times

posted on Wed, 01/06/2010 - 9:08am
Menno Mafait's picture

1) If you trust mathematics: No change!

2) You totally miss my point here: A fundamental change in genes is needed to form other species. However, genes only allow non-fundamental 'defects'. Any fundamental change in genes causes death of that organism.

So, I challenge Andrew to recreate evolution by Synthetic biology. I'm sure he will never succeed in this.

3) The radioactive decay of minerals can be determined, but it say anything the age of life.

Example: If I deposit 100 dollar each month on my bank account and redraw 101 dollar each month - the rate of my bank savings decay is 1 dollar per month. However, it doesn't tell me anything about my age.

4) Yes, genes only degenerate. Look around and see by yourself! All compound elements and structure decay! Also your 'specialisation' is a form of degeneration.

For evolution increasing complexity is required. However, all changes in genes are only caused by Natural Selection (Darwin) and Variety (George Mendel). Both - Natural Selection and Variety - causes only non-fundamental changes. And - again- if a fundamental change in genes happens - that organism will die.

5) I didn't state that ALL plants rely on bees. I wrote: "...some flowers decided...".

For a change is in the reproduction system of a species - a fundamental change in its genes is needed. And - again - any fundamental change in genes... death!

posted on Wed, 01/06/2010 - 3:40am

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