An Artificial Slice of Life

Lauran Neergaard breaks the story at the Washington Post:

Scientists announced a bold step Thursday in the enduring quest to create artificial life. They've produced a living cell powered by manmade DNA…

Scientists for years have moved single genes and even large chunks of DNA from one species to another. At his J. Craig Venter Institute in Rockville, Md., and San Diego, Venter's team aimed to go further. A few years ago, the researchers transplanted an entire natural genome - the genetic code - of one bacterium into another and watched it take over, turning a goat germ into a cattle germ.

Next, the researchers built from scratch another, smaller bacterium's genome, using off-the-shelf laboratory-made DNA fragments.

Friday's report combines those two achievements to test a big question: Could synthetic DNA really take over and drive a living cell? Somehow, it did.

Ms. Neergaard is lucky that bad science writing isn't a crime; otherwise she would be in shackles by now. The word "enduring" in the first sentence is puerile puffery. The much worse sin against scientific literacy is that DNA doesn't "power" living cells, nor does it "take over and drive" them. DNA is the fundamental repository of information for most of its operations and for the essential business of reproduction. DNA is a very powerful map, but the cell itself does the driving.

These distortions have clearly been encouraged by Venter, who is both a scientist and an entrepreneur. This is how he sells his science:

"This is the first self-replicating species we've had on the planet whose parent is a computer," Venter told reporters.

Well, not yet. Venter's team built the genome of one kind of bacteria from scratch, using fragments of DNA. In doing so, I gather they were plagiarizing the Lord's work by precisely copying the DNA of the cattle germ. Then they transplanted the artificial genome into a different kind of cell (a goat germ). The new cell was able to function and I gather it has reproduced. But the parent of the new cell is clearly the recipient cell, not the computer.

The distortions aside, this is a very big story. That a research team can assemble a complete genome from scratch is an astounding feat of technology. That the transfer of a genome into a cell changes the latter's species form is a fundamental bit of intelligence for metaphysics. What would happen if you replaced the DNA in a human cell with chimpanzee DNA? I am guessing you would get a chimpanzee cell whose parent was a human being.

It is the metaphysics that disturbs Alasdair Palmer at the London Telegraph.

[If Venter's technology] works for the cells of bacteria, it will work for our cells, too: with us, there are more components – we have 25,000 genes in each of our cells, as opposed to the 500 that control the reproduction of the bacterium that Dr Venter used – but the mechanisms are the same. The differences are a matter of quantity, not quality.

That sends a shiver down the human spine. What has happened to the mystery of life, the intangible, miraculous glory that we think is somehow its essence? It has disappeared. There are only molecules and the void.

Mr. Palmer is in way over his head here. We aren't human because we have more genes than bacteria. That's like saying that the only difference between a mud hut and the Metropolitan Museum of Art is the size of the blueprints. The human genome and bacterial genomes contain fundamentally different information.

But Mr. Palmer suffers from philosophical and theological illiteracy as much as from scientific illiteracy. Suppose you had to choose your sole reading material for the next five years from one of three boxes. One contains a blank book and a supply of pens. Another, the complete speeches of Barack Obama. The third, the complete works of William Shakespeare. You have to choose blindly. Would it comfort you to know that each box contains roughly the same number of ink and wood pulp molecules?

If you get the first box, you are in for a lot of boredom. If you choose the second, you will end up scratching your eyes out. If you choose the third, you will manage well enough, and come back with at least one bit of literary expertise under your belt. Venter's experiment confirms that there is much more in heaven and earth than mere molecules. There are forms and information.

As for theology, the teaching of the major churches over the last two millennia is that resurrection means the resurrection of the body. That would suggest that, just as Shakespeare's plays have to be substantiated in some physical medium to endure, so do human souls. I am quite comfortable with this, and in fact I think that no other view is coherent.

Mr. Palmer doesn't want to know the truth about the human soul because he doesn't really believe in the human soul. He wants to be safe in warm in his ignorance. Fortunately I have read Aristotle, with some care, and I am confident that biology is ultimately the study of souls. The more we know, the more we will be amazed and gratified.

Comments

[knowledge is power]

The article should have been titled as Synthia & Apollo and their Synthetic Life.

Synthetic/Synthia/Cynthia

http://www.urbandictionary.com­/define.php?term=Synthia

Cynthia or "Synthia" was originally an epithet of the Greek goddess of the moon, Artemis, who was sometimes called "Cynthia" because, according to legend, the goddess was born on Mount Cynthus. Known also as a master of animals. Parallel Greek goddess to Roman goddess Diana. Daughter of Leto and twin sister of Apollo.

Synthia & Apollyon are one in the same... The hermaphrodite beast of the book of Revelations as seen as Apollyon and the 'scarlet whore' named as Hel...

All you have to do is study the Apollo/Athena, whom is Synthia/Artemis, angle in every story/issue/matter, and you will find the source of the evil. Because the beast named as Apollo/Athena is at the core of EVERY evil ever seen down through ALL the eons and ages... That evil can be seen when the connected names are completed... They touch every evil ever known...

[Jim Meidinger]

Lab created life. What could possibly go wrong?

[BillW]

"One contains a blank book ... Another, the complete speeches of Barack Obama"

I was with you right up to this part. What is the difference between these two boxes again? I somehow missed it.

[Douglas Wiken]

Charlie Rose interviewed Venter a few nights ago. He was making things as simple as possible I assume. Made the analogy between DNA as the software of life. Then indicated that, as you indicate, whatever they made was generated by computers assembling the handful of chemicals in DNA.

I would guess he was hoping to get more support for his project by discussing possible applications of the technology to production now done by more or less natural and also inefficient means in chemical manufacturing, etc.

He indicated the research had taken 15 years of works by perhaps several Nobel-prize winning researchers. Many dead ends and false leads along the way. Only dogged pursuit kept them going. Even with all that, what they did was essentially still a proof of concept rather than a product useful in some other context. But, was strongly suggesting that the technology could turn out to be very much a profit-making application of the research.

http://www.charlierose.com/view/interview/8850

Would be nice if Rose and company did not charge an arm and leg for transcripts.

[Stan Gibilisco]

"Ms. Neergaard is lucky that bad science writing isn't a crime; otherwise she would be in shackles by now."

... and I should have been executed long ago, some would say.

"Lab created life. What could possibly go wrong?"

... Leave it to a lot of bad science writers, and, dare I suggest, a single rogue run of reality.

[Miranda]

I am reminded of the joke in which God and a scientist agree to have a man-making contest.

God says, "Now, we're going to do this just like I did back in the old days with Adam."

The scientist says, "Alright!" and he bends down to pick up a pile of dirt.

But God says to him, "No, no. You go get your own dirt!"

As long as we are still using what is already in creation, and as long as we still have unanswered questions, I don't think the mystery is destroyed. However,
one can certainly see problems with such advancements popping up along the way.

Because I have been watching Dr. Who lately, the first thing I thought of when I read this story, was the episode that featured the nanogenes. In this episode, the nanogenes have been bred to heal things, but when they come across a dead little boy wearing a gas mask, they aren't sure where he ends and the mask begins. As a result, they create a zombie-like monster when they attempt to put fix the boy. In fact, they create a whole brigade of such creatures.

Obviously, that's fiction. But I think it's entirely possible for scientists who are just beginning to "create" DNA to create flawed creatures and I suspect that if, somewhere down the road, someone were to try to create a human using this method,he mind end up producing something horrific.

[KB]

Miranda: Science fiction is very good at warning us about what might go wrong, but not so good at telling us how to avoid it. If I wanted to write a story in which human technology brings about the end of the world (the human world or even the living world), I would write about a very small thing rather than a Frankenstein, let alone a Godzilla. A voracious artificial microbe that gobbles up oxygen, or protein, or something like that, that would be terror from the test tube.

I run into two obstacles when thinking about what to do. One is that I don't know how to foreclose such a possibility without shutting down science altogether. The other is that nature is constantly carrying on such experiments on its own. If I understand the science correctly, our oxygen-rich environment is not the original environment. When oxygen producing microbes first appeared, they poisoned the atmosphere for almost all the previously existing organisms. Big disaster, except that it made us possible.

To live is to risk. To think and tinker is to take big risks. Here, Buddha comforts me. Everything that exists exists because something else fell the heck apart. There is no way out of that. The good news is that, just now, waffles are possible.

[Miranda]

It is probably true that we cannot eliminate the possibility of scientific disasters without shutting down science. But this does not mean that we cannot keep our eyes open or that we should not try our best to prevent such disasters from happening. The fact that science fiction doesn't always tell us how to deal with problems is not an excuse.

Furthermore, I am not sure that I agree that everything exists because something else fell apart. My belief in the existence of God makes that seem unlikely. And even an atheist would probably conclude that whatever fell apart first must have existed for another reason.

Nevertheless, I agree with your main point, and I appreciate the things that fall apart to make waffles what they are.

[KB]

Miranda: One of the many reasons I love you is that you keep driving me back to the main question. "Quid Sit Deus," as Leo Strauss put it. "What might God be?" Or as Martin Heidegger put it: "why are there existing things rather than nothing?" Neither question is answerable by philosophy, and so both set the limits which define philosophy. The Buddha stands alone among the founders of the great missionary religions (Paul and Mohamed)in so far as he remained within those limits. Looking at the world as it presents itself, everything that exists exists because something else fell apart.

I agree that we ought to keep our eyes open. I am all about that. I also agree that we ought to try to prevent disasters. I am just not sure how we do that, short of shutting down research.

[Miranda]

Are we sure that philosophy can't answer these questions and if not - why not?

A wise professor once defined philosophy to me as "The thirst for knowledge."
I suspect that a thirst for knowledge might very well uncover the answer to these questions, though perhaps it hasn't done so sufficiently yet. Giving up on the question, however, seems rather anti-philosophic.

And I confess to being a little puzzled about what you mean by "the world as it presents itself." Does this mean that we can only look at the visible? Do we ignore theories and only focus on what we can tangibly prove to ourselves? Or do you mean something else entirely?

[KB]

I can't be sure that philosophy can't answer those questions just as I can't be sure that I won't win the lottery. I do have strong hunches about both.

Philosophy is indeed the thirst(Socrates called it "erotic") for knowledge, but only by one method: the pursuit of what is knowable by relentless questioning. If the world (meaning all rationally knowable things)is complete and self-contained, then philosophy might arrive at the end at wisdom. But I can't see how that we could know that the world is like that, and even if it is, why does it exist and why is it what it is? Biblical religion poses precisely the thesis that something unknowable created all that is knowable. How can the pursuit of what is knowable verify or refute the unknowable? I am not saying we should give up on these questions, but it is not anti-philosophic to recognize the limits of philosophy.

The world "as it presents itself" emphatically includes theories. The other day I saw a creature in my yard that looked and acted like a rabbit. I have a theory about that: it was a rabbit. Geologists have a theory about Devil's Tower: it is the result of the processes by which things emerge and then suffer erosion. That theory is based precisely on the same processes and forces we see action every day. On the other hand, the Native American story (not a theory) that the mountain was clawed by a giant bear includes something that no one has ever seen: a giant bear. The world does not present with giant bears.

Theories can certainly model what is invisible: molecules, plate tectonics, the common ancestry of human beings and chimpanzees. These are theories, as opposed to other kinds of stories, because they are rooted in observations and hypotheses that can be tested by observation. Physics, geology, and evolutionary biology try to understand the invisible (including the past) in terms of what is visible now. They assume that the same forces that are in action now were in action everywhere and always. But how does one prove that that is true? The passionate search for knowledge assumes that the world is intelligible. Every act of science and philosophy may be said to test that assumption, but it can never be confirmed.

[Miranda]

I concede the point about the limits of philosophy, although the study seems somewhat duller when framed in such a way. I prefer the idea of a passionate, limitless search for answers over a series of limited questions, designed to answer only what fits inside certain boundaries. Still, if that really is what philosophy is, then I can't argue its definition away.

But I can and do take issue with your idea that the biblical religion paints God as unknowable. In fact, it does the opposite. In the New Testament, we have verses such as these:

John 10:13, "I am the good shepherd, and know my sheep, and am known of mine."
Luke 4:8, "Draw near to God and He will draw near to you."

In the Old Testament, God is knowable as well.
It says things like the following:

Jer 24:7 And I will give them an heart to know me, that I [am] the LORD: and they shall be my people, and I will be their God: for they shall return unto me with their whole heart.

Jer 31:34 And they shall teach no more every man his neighbour, and every man his brother, saying, Know the LORD: for they shall all know me, from the least of them unto the greatest of them, saith the LORD: for I will forgive their iniquity, and I will remember their sin no more.

I am not a biblical expert, so I may be wrong, but I cannot think of a place in the bible that says that God is unknowable.

Furthermore, I am not sure the idea of a giant bear is so far fetched.

If we can observe the Devil's Tower and theorize that it has eroded because we know that other things do, then why can't look at the bears of our time, compare them to the fossils of Ursus spelaeus (the giant, extinct cave bear), and conclude that since bears have, indeed, gotten smaller over time, there may very well have been a giant, tower-scratching bear at some point in time?