Re-designing Bacteria
by MikeGeneFrom here:
Justin Gallivan, PhD, assistant professor of chemistry, and graduate student Shana Topp successfully reprogrammed E. coli's chemo-navigational system to detect, follow and precisely localize to specific chemical signals. In doing so, the scientists exploited E. coli's natural chemotaxis, a microbe's ability to move toward specific chemicals in its environment.
"Equipping bacteria with a way to degrade pollutants, synthesize and release therapeutics, or transport chemicals with an ability to localize to a specific chemical signal would open new frontiers in environmental cleanup, drug delivery and synthetic biology," says Dr. Gallivan.
["¦]
Chemotactic bacteria navigate chemical environments by coupling their information-processing capabilities to powerful, tiny molecular motors that propel the cells forward.
Researchers have long envisioned reprogramming bacteria so that microbes capable of synthesizing an anti-cancer drug, for instance, can be used to target diseased cells while sparing healthy cells of side effects. Likewise, scientists are researching ways to use bacteria to clean up oil spills or remove other pollutants from soil, water and wastewater.
"This new ability to equip motile bacteria with a precise and tunable chemo-navigation system will greatly enhance the impressive arsenal of natural and engineered cell behaviors," says Dr. Gallivan.
Such research teaches us two things.
May 12th, 2007 at 12:24 pm
"MikeGene: 1. Design and evolution can indeed co-exist. To sufficiently account for the existence of these bacteria, we must appeal to a) their evolutionary history and b) the researcher's design. This may seem too obvious to have to point out, but given that so many think that design is somehow contradictory to evolution, it is important to establish this principle of co-existence."
It shouldn't need to be said, but it is. It is good to point it out and make it plain.
It is too, too easy in our bumper sticker, entertainment framed, sound-bite culture to say that ID is an "alternative" to evolution — as if it were a one-for-one drop in replacement. The "alternative" meme fits with a simplistic all-or-nothing treatment.
I believe it would be more accurate and more helpful to consideration if people could understand the ID inference as clarifying the limiting boundary around what unguided natural processes can accomplish on their own, in distinction from what intelligent agents can do. The ID inference rests entirely upon this distinction in effects.
That should never be taken to imply that unguided natural processes cease to function or to affect life. All or nothing thinking is a bane to constructive communication on this topic.
Comment by eric — May 12, 2007 @ 12:24 pm
May 12th, 2007 at 4:59 pm
I hate to think how something like this might be used for ill in the wrong hands, but no doubt someone will think of it.
I wonder if our forensics will be able to tell the difference between "man-made" and "natural."
Comment by Mung — May 12, 2007 @ 4:59 pm
May 12th, 2007 at 7:14 pm
Hi Mike.
I clicked on the links as I usually do to see things in context and where they are coming from.
When I read the conclusion ("two things") I thought it was an accurate and balanced summary. So balanced in fact, I scrolled up to see what respectable science-based blog this came from. It was yours (I hadn't realized where I was).
Regards,
TP
Comment by Thought Provoker — May 12, 2007 @ 7:14 pm
May 14th, 2007 at 11:45 am
Design is not a live possibility. Analogies regarding complex specified systems, such as automobiles, planes and computers are valid only because we understand that humans can design such things and because we have some knowledge about the designers in question. In contrast, we have no examples of humans designing any living system in the biological world and we have no knowledge about the potential designer of such systems. Thus, analogies to design fail as they relate to biology.
Wait, what's that? Humans are involved in reverse engineering and reprogramming living systems?
Well shoot, there goes my objection to a design inference in biology . . .
Comment by Eric Anderson — May 14, 2007 @ 11:45 am
May 14th, 2007 at 12:05 pm
Why do we need to appeal to their evolutionary history? This form of design seems to work just fine without knowing what the history of the bacteria is, and design ought to be inferrable without a complete history.
Comment by chunkdz — May 14, 2007 @ 12:05 pm
May 14th, 2007 at 12:20 pm
Hi chunkdz,
Mike Gene wrote…Design and evolution can indeed co-exist. To sufficiently account for the existence of these bacteria, we must appeal to"¦ their evolutionary history.
You asked…
Because there is value in trying to make a single, MUTUAL OMA model.
The alternative is a shoot-out at the O.K. corral. Sure, 2 billion followers who are inclined to accept a designer hypothosis can make it the scientific "truth" by fiat. However, that will mean you will be doing what you are accusing the "other side" of doing.
Provoking Thought
Comment by Thought Provoker — May 14, 2007 @ 12:20 pm
May 14th, 2007 at 12:47 pm
TP
I don't have a problem with that.
I don't have a problem with that either.
Uggh. Are we seriously going back to the ID = creationism meme? Unless you are willing to evaluate ID on it's merits and forego the stereotypes you are effectively cutting off rational discourse.
Why don't we let Mr. Occam decide? As materialist explanations get wilder and more fanciful, design inference becomes more rigorous, and more soberly evident.
In my opinion we already have OMA. The intersection is called truth.
Comment by chunkdz — May 14, 2007 @ 12:47 pm
May 14th, 2007 at 1:41 pm
Why would evidence of common descent be evidence against intelligent design? Wouldn't it, rather, be evidence for intelligent design, if anything?
The implicit idea in the evolutionary naturalist's claim seems to be that an intelligent designer would have created each species or at least each phylum separately, and wouldn't have created them by means of an evolutionary process .
But why suppose such a thing? Is there any scientific evidence that if some intelligent agent wishes to design something, such as a computer capable of performing various valuable tasks, it won't do so using the most parsimonious program or set of instructions, but will necessarily or at least more probably write lots of completely discrete programs instead? My strong intuition would be to say the opposite is true.
If life is as reasonably widespread in the universe as many naturalists believe it to be, but also dependent on non-intentional events rather than design, we would be more likely not to find evidence of common descent, but rather evidence that today's observed species were descended from uncommon ancestors who were widely separated in space and time.
Also, it is not a good objection to say that we 'know' that buildings and computers and computer code are intelligently designed because we can see people at work doing the designing, and that this is why those cases are different from the evolution of species case. Because in fact we do not physically observe anyone's intelligent consciousness. What we literally see when we look at a computer scientist or architect at work is complicated material bodies in various states of mathematically intelligible motion. That's also what we see when we observe any life form or investigate its history. In other words, the cases of intelligent design that we 'know' about are no different in terms of physical observation from the cases in biology, except for the precise form and kinds of complexity involved.
If the 'we know buildings etc are the result of intelligent design' claim is taken as a genuinely scientific statement or at least as derivable from scientific statements, there must be a scientific way of making precise what types of material motions and complexity of structure and function license an inference to intelligent design, and what types do not.
If the answer is, 'involved use of a human brain', then it's trivially true that living species were not intelligently designed. But unfortunately, that definition, as well as ruling out God as the creator, also rules out there being any intelligent designers elsewhere in the universe.
That, if true, would be news to many.
Comment by stunney — May 14, 2007 @ 1:41 pm
May 14th, 2007 at 2:28 pm
"Such research teaches us two things.
1. Design and evolution can indeed co-exist"¦"–Mike Gene
But, as you suggested, not merely "co-exist." One cannot truly be understood w/o the other. They don't just "co-exist," but are necessary compliments to anything that reasonably and truly approximates reality.
(Therefore anyone, IDer and critic alike, who thinks in "either/or" terms are to be dismissed airly.)
"It is not so difficult to discover that both evolution and intelligence use the same set
of techniques: Both transform real experiences into symbolic representation and keep
the messages in a well-organized, computationally efficient form; use these messages
for searching groups of similarity and generalizing them; repeat this generalization recursively
so that the nested hierarchies of efficiently organized information are being
developed; increase their efficiency by focusing attention upon limited subsets of information;
and use searching processes to combine elements of this information into
messages that could not be obtained from the experiences."
From the Preface to Meystel & Albus' "Intelligent Systems: Architecture, Design, and Control." Wiley. NY. 2002.
Interesting how both comparative and historical methods will fail us to make such a design/evolution distinction…
(Btw Gallivan has patented an evolutionary design technique. But are natural materials and processes patentable? Sounds like a legal question that IDers and their critics just love to munch!)
Comment by Rock — May 14, 2007 @ 2:28 pm
May 14th, 2007 at 4:00 pm
Hi chunkdz,
You wrote…
I am working towards the "so what?" meme. So what if you are inclined to think a creator/Intelligent Designer/God is involved? It shouldn't matter under OMA. Let's work this through and see if it fits in with existing evolutionary thinking. Your comments imply an out-with-the-old-in-with-the-new attitude. As for cutting off rational discourse; you wouldn't be the first person to define "working together" as "my way or the highway" (it happens a lot in Washington D.C.).
I need to get back to work so I have to be blunt about "Mr. Occam" and "truth". Last Thursdayism provides a simple truth. Should we go with that? If not, why not?
Provoking Thought
Comment by Thought Provoker — May 14, 2007 @ 4:00 pm
May 14th, 2007 at 5:43 pm
Thought Provoker wrote:
Because it's irrational. I know that may come as a shock to you, but it's true. A truly vast number of mental states would be false if Last Thursdayism is true. Reason itself would be felled, mortally wounded.
You are just going to have to suck up the fact that no such consequence follows from theism. So your attempt to suggest that theism and Last Thursdayism are intellectually equivalent is supported by literally nothing other than your stubborn, empty-headed bravado. Which is why no sane and seriously bright person in recorded history has believed in Last Thursdayism, whereas many sane and seriously bright people have been theists. It's an intellectually fraudulent and merely rhetorical tactic to suggest otherwise.
So I call bullshit on your bullshit, TP. No sane and seriously bright person believes your bullshit about Last Thursdayism. You're attempting a counterfeit of reason. You're an intellectual fraud.
So, it's time to let the flies have at it, thus sending a coded signal that you were there.
Comment by stunney — May 14, 2007 @ 5:43 pm
May 14th, 2007 at 7:00 pm
TP
They do?
It does?
Comment by chunkdz — May 14, 2007 @ 7:00 pm
May 14th, 2007 at 7:54 pm
Hi Stunney,
While I suspect a few people would rather I leave this malodorous comment alone, I feel compelled to react.
I wrote… "Last Thursdayism provides a simple truth. Should we go with that? If not, why not?"
You responded…
Is Last Thursdayism irrational or lacking in common sense?
Our perceptions tells us that the sky is up and the ground is down. That the sun is moving, not us. We perceive the universe revolving around us.
Reason isn't "mortally wounded" by questioning our perceptions, it is strengthened by it.
Is reason based on popularity?
Last Thursdayism is an abstraction that helps separate reason from assumptions. I do not offer it as an equal. If I wanted to do that, I would have talked about supernatural science fair projects. Of course Last Thursdayism isn't equal, it's much simpler.
Joy talked about that clear lines in the sand where everything on the other side is unknown and unknowable. I believe it is reasonable and useful to consider there are multiple Truths on the unknowable side of the NOMA line since no one knows the Truth and no one will, by definition. We can all live in peace. Even the rare few that believe in something as unusual as Last Thursdayism.
Claims of unique knowledge of the unknowable, even by logical argument, is a violation of NOMA. If you violate NOMA, I can violate NOMA by my code of ethics. Now we can either try to work out a common OMA model or we can do battle.
Are we doing battle or not? Tactics are part of war and if what I say is intellectually fraudulent, you should be able to show why without resorting to emotional bombast.
Do you feel better now?
Provoking Thought
Comment by Thought Provoker — May 14, 2007 @ 7:54 pm
May 14th, 2007 at 8:13 pm
Hi chunkdz,
Your last comment was referencing my answer to your..
…question. Hopefully, you understood my answer (whether or not you agreed with it).
Let me revise the sentence you took out of the middle of a paragraph…
"In my opinion, your comments imply an out-with-the-old-in-with-the-new attitude."
If you are interested in why that is my opinion, let me know and I will explain.
As to Last Thursdayism's status as "truth". That was the point. I don't know the Truth (capital "T"), do you?
Provoking Thought
Comment by Thought Provoker — May 14, 2007 @ 8:13 pm
May 14th, 2007 at 9:09 pm
Hi chunkdz:
The human designers reprogrammed bacteria that they snatched from Nature. Unless these bacteria were very recently deposited on the planet from a non-human designer, they have an evolutionary history (even if they ultimately owe their existence to non-human design). The bacteria themselves thus exist because of a) human design and b) evolution. That design and evolution can co-exist means that no law of nature is violated in postulating a non-human design further back in deep time.
Comment by MikeGene — May 14, 2007 @ 9:09 pm
May 14th, 2007 at 10:23 pm
TP
If you don't mind. I'm confused as to why you would characterize me as a "my way or the highway" kind of person. Especially when I began our conversation by saying I don't have a problem with OMA, and I don't have a problem with the "shootout" version. In other words, I'm not the one with the problem.
I know that scientific naturalism does not care what the truth is, and that religion cannot, as you say, "make scientific 'truth' by fiat".
Capital "T" or little "t", we can only determine truth where religion and science intersect. It's a narrow overlap in my opinion, but if you were really interested in finding it, you wouldn't resort to mischaracterizations.
Comment by chunkdz — May 14, 2007 @ 10:23 pm
May 14th, 2007 at 10:31 pm
MikeGene,
I had forgotten that you attribute much more creative power to RM + NS than I am inclined to. In light of that, I can see your point about including evolutionary history.
Is there a limit to what RM + NS can accomplish, in your opinion? If so, where do the boundaries lie?
Comment by chunkdz — May 14, 2007 @ 10:31 pm
May 14th, 2007 at 10:36 pm
Hi chunkdz,
For me, it's not about limits and boundaries. They may indeed exist, but I'm not confident enough to declare any. Instead, I'm more interested in whether there is good evidence to think RM + NS are indeed the "designers" of such an easily reprogrammable system. That's where point #2 comes in. After all, an easily reprogrammable system might just be what the designer ordered when having to take RM + NS into account.
Comment by MikeGene — May 14, 2007 @ 10:36 pm
May 15th, 2007 at 9:41 am
TP:
Um… slight correction, so as not to promulgate misunderstanding. It's known, unknown *OR* unknowable. There is no easy way to distinguish between unknown and unknowable, but there is reason to suspect that human mind - complete with imagination, dreams, mythologies, etc. is the ultimate arbitor. At least, for as long as we're human.
IOW, if we can think and wonder about it, it's probably under the table somewhere waiting for us to reach in and grab it, put it right up there next to the centerpiece or in its place in the table setting. If it never occurs to us, it's off in a corner somewhere in unknowable land, never to make its way close to the table.
There are certainly stranger things than Last Thursdayism out there, some of them proposed by scientists. I agree we can live peaceably. But I do not agree that metaphysical beliefs are necessarily 'unknowable'. I suspect the most consistent metaphysical formulations' truth value is merely 'unknown'.
This is the danger of calling all metaphysical formulations 'unknowable' if they're actually just 'unknown'. I mean, if one is disposed to believe we have evolved, one must generally accept the evidence of our historically recent appearance as well as evidence that it's our brains/minds that evolved fastest and most uniquely. We've no reason to believe our evolution is not ongoing, and we've no grasp on what else may be directly perceivable in the future that is not directly perceivable now.
…depends entirely on how many colors there actually are in reality, so to speak. Red didn't magically pop into existence when our simian ancestors developed the equipment to see red. It was there under the table all along - we just didn't know it.
Comment by Joy — May 15, 2007 @ 9:41 am
May 15th, 2007 at 9:46 am
Hi Chunkdz,
You wrote…
If you haven't noticed, I like to debate/argue. I am provocative enough that I could be labeled a "troll" with some justification. I wrote… "you wouldn't be the first person to define 'working together' as 'my way or the highway'" as a warning where your kind of logic might lead, not as a (mis)characterization of you as a person. In fact, I wrote that based on the assumption that you are not the type of person that would knowingly do such a thing (it would bother you).
That being said, you followed up with"¦
You do have a problem if someday you want to claim ID is a better scientific explanation for evolution than prevailing theories. Your problem is often called "burden of proof".
You also wrote…
My knee-jerk reaction to your use of a "narrow overlap" was to ask "You mean like the sharp end of a wedge?". You have bring up a concept I don't remember anyone else stating in the two NOMA threads. Some people see NOMA as limiting scientific intrusion into religion. Some people see NOMA as limiting religious intrusion into science. But this is the first time I think anyone has postulated a middle no-man's land that can't intrude either.
At the risk of being provocative and/or mischaracterizing again. If you aren't suggesting something that will ever be pertinent to either the religious or the scientific magisteria, why bother?
While MikeGene maintains that ID isn't science (yet), he is making very good scientific arguments for looking at scientific data in a new light. I tread on very shaky ground to make any assumption of what Mike is doing, but I suggest he expects that someday the scientific magisteria will have to include ID aspects in its scientific theories.
I agree this is the best approach assuming I haven't "mischaracterized" his position.
Provoking Thought
Comment by Thought Provoker — May 15, 2007 @ 9:46 am
May 15th, 2007 at 9:55 am
Hi Joy,
I would love to discuss your last comment at length. It was very well stated.
However, I don't think my client will understand why I spent the day arguing with you instead of fixing his problem. If the hotel's internet is up and working I would like to respond more fully. Would it be better here or in the last NOMA thread?
Mike, if you see this. Do you have an opinion as to which thread?
Regards,
TP
Comment by Thought Provoker — May 15, 2007 @ 9:55 am
May 15th, 2007 at 11:56 am
TP
Thanks. Why bring it up then?
I think it's already as good a guess as any out there, if not a better one. But there's that pesky word "proof". It implies an underlying truth, something which neither religion nor science can lay independent claim to. Let's face it, if this were the mid 17th century, the NCSE might have been defending the theory that maggots emerge endogenously from meat. They would claim to have a mountain of meaty, slimy evidence - but they would not have absolute proof, and they certainly wouldn't have truth.
Yup, that's pretty knee jerk. But I always thought of it as more of a narrow gate that few pass through.:wink:
Well, I didn't say that either. I said it was a narrow overlap between the two.
But in short what I am suggesting is that the best chance that we humans have of ascertaining truth lies where religion and science are in agreement, and mutually support one another.
Comment by chunkdz — May 15, 2007 @ 11:56 am
May 15th, 2007 at 5:58 pm
TP - I responded in the Provoking Thought thread.
Comment by Joy — May 15, 2007 @ 5:58 pm