TelicThoughts

Politics isn't a focus of this forum, and participants here cover the spectrum of political views and policy leanings. This is not a thread about politics, please don't use it as one.

That out of the way, I'd like to post a few excerpts from a review of progressive activist Markos Moulitsas' new book Taking On the System, because his words have broader social application.

This review was penned by Al Giordano. I think many here will find parallels to the bad old Culture War in this neck of the woods. For instance, here's a citation from the book that if you squint your eyes a little bit, should speak loudly to ID's struggle against the gatekeepers of NDS orthodoxy…

"I started the site [DKos] for a simple reason - I felt ill-served by the undemocratic gatekeeping mentality so prevalent in our society. And, at that time, we seemed to be on an inexorable march toward war with no avenue for dissent. There was an assumption by the powers that be that the rest of the citizen body couldn't think for ourselves. That we needed self-appointed and so-called experts to tell us what to think, what to do, and what we should - or should not - know. For far too long, these gatekeepers controlled the national conversation."

To which Giordano adds in his own view…

Kos expands his anti-gatekeeper view of politics to other key sectors of society: the media, the music industry, and Hollywood among them. Don't presume that this is a book about Democratic Party politics: It is only marginally so. It's about organizing in any and every field where creative individuals and communities must learn to bypass or to crush the self-appointed wardens…

Italics mine. Giordano includes a summary from chapter five entitled "Feed the Backlash," that could easily be applied elsewhere…

"When your enemies begin to notice you - and attack you - you have arrived. Instead of avoiding confrontation with gatekeepers and opponents, embrace it and feed it. Stoking the flames of controversy brings visibility to your issues, raises your profile and effectiveness, and begins a cycle of ever-increasing attention that you can use to your advantage."

In this thread I'd like to see some thoughts on the legitimacy of organized tactics for the purpose of challenging the status quo anywhere a status quo (a.k.a. "orthodoxy") maintains a cadre of gatekeepers to keep dissent at bay. And some thoughts about whether the status quo being challenged has much room for whining about organized tactics if they've an arsenal of organized tactics themselves to serve their gatekeeping function.

In his book, The Edge of Evolution; the Search for the Limits of Darwinism, Michael Behe cites work by Barry Hall in support of his view that there are limits fairly narrow limits to what Darwinian evolution can accomplish:

But antibiotics that require multiple changes are far more resistant to Darwinian processes. That's a critical fact to understand, too. Malaria requires several mutations to deal with chloroquine, so it's a far better drug than ones that are stymied by a single mutation. And chloroquine is not the only case. Recently, former University of Rochester microbiologist Barry Hall examined various antibiotics in a class called "carbapenems," which are chemically similar to penicillin.[26] With unusual clarity of thought on the topic of evolution, Hall wrote, "Instead of assuming that [the chief kind of enzyme that might destroy these antibiotics] will evolve rapidly, it would be highly desirable to accurately predict their evolution in response to carbapenem selection" (emphasis added). Using clever lab techniques he invented, he showed that, although most of the antibiotics quickly failed, one didn't. The reason is that neither single nor double point mutations to the enzyme allowed it to destroy the certain antibiotic (called "imipenem"). Wrote Hall, "The results predict, with >99.9% confidence, that even under intense selection the [enzyme] will not evolve to confer increased resistance to imipenem." In other words, more than two evolutionary steps would have to be skipped to achieve resistance, effectively ruling out Darwinian evolution.

(p.236-237).
[26] Hall, B.G. 2004. In vitro evolution predicts that the IMP-1 metallo-beta-lactamase does not have the potential to evolve increased activity against imipenem. Antimicrob. Agents Chemother. 48:1032-33.

I haven't read Hall's paper, so I'm taking Behe's word on how to interpret it. If the interpretation is correct, then it sounds like Hall is confirming where Behe thinks the edge of Darwinian evolution is. If correct, this could have profound consequences for medical research. We would only need to find drugs that require more than two evolutionary steps in order to bestow guaranteed resistance to bacteria.

Is Behe's interpretation of Hall correct? If so, is Hall right? Does that make Behe right? I'll be on vacation for a week. Please stay on topic. I'm curious what the critics have to say on this. I'll read it when I get back.

Telicmeme posted Life's toolkits at his blog Teleomechanist. The blog entry references quotes about stem cells and arrives at this comment:

So stem cells have a built-in toolkit that responds to random changes, enabling then to respond to changes in their environment in a systematic and controlled way, ultimately leading to just a few endpoints. The toolkit harnesses random variation and selection to reach the same destination. The stem cells are front-loaded (provided with a toolkit) to develop along a certain path while harnessing random variation and selection.

He then cites an immunological function that entails induced mutations of the DNA of B lymphocytes and makes this comment:

B lymphocytes have a toolkit that regulates mutations for the purpose of generating antibodies. Thus, here we have another toolkit that harnesses random variation and selection to intentionally generate variety for the purpose of producing novel antibodies.

How many more toolkits that harness quantum randomness and selection to generate controlled variety will we discover?

More than we anticipate I suspect.

LHC to Start Up September 10

I have expressed some interest in High Energy Physics and various QC, GUT and SUSY theories on occasion. There are several Swamp denizens (including one doing double duty as commenter here and peanut gallery heckler there) who strongly believe that I have no right to be interested or business following theories and developments at that end of physics. I beg to differ.

Why, anyone interested in what science knows or doesn't know about the nature of nature and/or any part of nature (and what they're doing to plug holes in their knowledge) might find the theories and experiments of HEP of great interest and entertainment value. I figure that when I have no business or right to know what's going on in theoretical and experimental physics, they'll stop reporting what's going on in theoretical and experimental physics. A situation none of us should welcome.

Fortunately, the public still has a right to know some or most of what's going on (at least at the public funding level), and an entire scientific press corps out there attempting to give people information that they can understand if they try. Perhaps those with a bit of background physics will follow with less effort, but if the interest is there, effort is a fair investment. For those interested, here's where things are at as of August 12, 2008…

I am happy to report that the "cool down" phase of powering up the Large Hadron Collider at CERN should be done by now, as all eight sections of the beam tubes housed in a 27-kilometer torus reach their operating temperature of -271ºC (1.9º above absolute zero). Synchronization testing for the magnets was scheduled to begin last weekend…

…Tests will continue into September to ensure that the entire machine is ready to accelerate and collide beams at an energy of 5 TeV per beam, the target energy for 2008. Force majeure notwithstanding, the LHC will see its first circulating beam on 10 September at the injection energy of 450 GeV (.45 TeV).

If all goes well and stable circulating proton beams are established, they'll be brought into collision and the power will be increased to 5 TeV per beam before the end of the year. Though the LHC is not planned to operate in the winter (ski season and all), I imagine this first one will be non-stop. Scientists are hoping to eventually yield collision energies of ~14 TeV. The $8[+] billion dollar machine will provide many years' worth of sub-atomic fun for beam jockeys, megacomputers chock full of data for research teams all over the world to pour over for many more years, and - hopefully (or not) - some lovely new beasties to befriend. Including Wiggly Higgly, whom they're about 95% certain will pop in to visit on a fairly regular basis in the six detector-shrouded target zones.

In fact, the LHC offers some of the very same concerns in and out of the HEP community that Brookhaven's RHIC provoked awhile back - you remember, the possibility that a 'strangelet' might be created that would cause a universal phase shift, alter the false vacuum state and/or otherwise bring an immediate end to all things. Or just produce voracious micro/mini-holes that would sink to the core and consume the planet, a much lesser danger because it would only destroy this solar system. Luckily (or not), the wigs at Brookhaven decided the risk was worth it because… um… they have a machine that offers such cool risks. Why in the world would any human object to that?

Multiply the energies a few times and the concerns don't go away. We are reassured by the confident hypothesis that RHIC's 2005 "fireball" - theorized to have produced a double micro-hole - evaporated in mere femtoseconds even after sucking up a goodly amount of matter that simply disappeared from existence completely, never to be seen or heard from again. Hawking radiation thus being "proved," they say, because the earth's still here. So long as there's a sub-theory out there somewhere that accounts for something and assures everyone it's harmless, then by gum, it's all harmless. Don't Panic.

LHC makes no bones about it, they're going for black holes on purpose (also hoping for monopoles and strangelets). They're also dismissive of concerns, as is of course expected. They figure that if THEY can produce such odd beasties, then the earth is already chock full of 'em due to high energy cosmic ray bombardment. What they're more excited about is the opportunity to directly study "TeV-scale gravity" and the predicted extra dimensions of spacetime that come with. Establishing the nature of mass is not the first or most interesting goal of the project. If Higgs exists, he'll show.

Compared to that, the tiny risk to humanity, the planet and solar system, the galaxy and all other things that currently exist in spacetime is more than worth it. We already know The Answer - it's 42. What we're inventing now is the question!

Much Easy-to-Understand LHC Info
CERN
ALICE Heavy-Ion Portal
M-theory, formerly known as Strings
The Story of Strangelets
MSNBC: Doomsday fears spark lawsuit over collider

Accurate replication of DNA is an essential component of cellular replication. There are multiple proteins which enable the DNA replication function. The process contemplated is that which occurs in unicellular organisms. I don't wish to bore the science experts who can't wait to enlighten the rest of us as to how the individual components of the DNA replication function gradually evolved. So I'll simply identify some important steps for instructional guidance purposes as well as proteins associated with them.

Replication must begin somewhere. Why not at the origin of replication with the formation of a replication fork. A prepriming complex of proteins forms. Included are DnaA proteins and single stranded binding proteins. Also involved are DNA helicases to separate the strands, DNA topoisomerases to respond to supercoils, DNA polymerase and DNA ligase.

Don't bother making semantic arguments about how to define irreducible complexity. There are multiple parts needed for function. The challenge lies in demonstrating the incremental evolution of these components. Judging by previous comments this should be a piece of cake. Identify pathways which include precursor functions and a functionally logical sequence of events supported by empirical data. Identify interpretation of data and distinguish it from the data itself.

I deleted the open letter to Dembski. It occurred to me that it was the type of thing that would fit in better at UD, instead of at TT. Sorry it took me so long to see that. But Raevmo asked a great question:

Bilbo, how do you know Dr Moon is a false Messiah?

I don't know if the following discussion belongs at TT. If you guys would prefer that I move it to my own blog, I can do that. No offense will be taken.

In chapter 13 of Mark (and chapters 24 of Matthew and 21 of Luke), Jesus tells his disciples that the Temple will be destroyed. They take this as an indication of the end times and ask Jesus when this will happen. The very first thing he tells them is, "Watch out that no one deceives you. Many will come in my name, claiming, 'I am he,' and will deceive many.[v.6]….At that time if anyone says to you, 'Look, here is the Christ [Messiah]!' or, 'Look, there he is!' do not believe it. For false Christs [Messiahs] and false prophets will appear and perform signs and miracles to deceive the elect — if that were possible. So be on your guard; I have told you everything ahead of time.[v.21-23]….At that time men will see the Son of Man coming in clouds with great power and glory." [v.26]

And in Matthew's version we have, "So if anyone tells you, 'There he is, out in the desert,' do not go out; or, 'Here he is, in the inner rooms,' do not believe it. For as lightning that comes from the east is visible even in the west, so will be the coming of the Son of Man." [24:26-27]

I quoted Mark first, because most New Testament scholars consider it to be the earliest of the four Gospels, with many dating it around 60 to 65 C.E. Some date it as early as 50 C.E. Some date it at 70 C.E. [Most scholars agree that Matthew and Luke wrote their accounts later than Mark's, dating them from 70 to 90 C.E., and it is believed that they largely based their own accounts on Mark's Gospel and also on another source that is referred to as "Q." The Gospel of John is ususally dated 90-95 C.E., and doesn't record Jesus's teaching on the end times.] Since most scholars think Jesus died around 30 C.E., this gives us a time frame of somewhere between 20 to 40 years after his death. That's not that long a time period. For those of you who are old enough, remember back 20 to 40 years to someone you either knew personally, or some famous person, and ask yourself what you can remember about them and what they said. And in the case of Jesus, we almost certainly had people continually preaching and teaching about things Jesus said almost from the time that he died. So when Mark eventually wrote it down, he was writing down things that were generally agreed to have been said by Jesus.

What I find most intriguing about what Jesus is supposed to have said in the passages I quoted, is that he said them at a time when he was not yet a "superstar." There would be no obvious reason to think that anyone would claim anything "in his name" at all. Why should they? If I said, "I come in the name of Joe Schmoe," you would all say, "So what? Who the heck is Joe Schmoe?" If Raevmo told us, "Someday someone will come in my name and claim to be the world's greatest scientist," we would say, "So what? We knew you had a big head, anyway." "No, no. Not me," says Raevmo, "Somebody else." And we would say, "Why would anybody come in your name, claiming to be the world's greatest scientist? Why wouldn't they just use their own name?"

Likewise, we could have said to Jesus, "Why would anyone come in your name, claiming to be the Messiah? Your just a country preacher from the sticks, who's going to be crucified in a few days. Why would anyone even remember you in a few years? And why would anyone want to associate themselves with you?"

So for Jesus to say something like this about himself either indicates that he had a very large ego, or that he had some inkling of the impact he would have on history, and that hundreds and thousands of years later he would be the archetype of the Messiah. He would be the one would-be messiahs would try to identify with, in one way or another, to get people to follow them.

So what is it about Jesus that made him special? Certainly his reputation as a miracle worker. Certainly the claim that he rose from the dead. But I think it's more than that. I think we instinctively trust Jesus. Even if we don't believe he ever performed miracles or rose from the dead. Even if we don't believe that he was the Messiah or the Son of God. There is something about Jesus that we trust. We know that he wasn't out for power. He wasn't out to get rich. He wasn't out to become famous. And I think that's what makes many people vulnerable to false messiahs. People such as Moon come claiming to be Jesus or from Jesus, and there is a desire to believe them.

And I think Jesus knew we would be vulnerable and that this would happen. Which is why it is the first thing he warns us to watch out for. And how will we know that they are false messiahs? Because they want power. Because they want to get rich. Because they want to become famous.

Jesus told us, "Don't worry. If I'm coming back, it'll be as big and as fast as lightning. You won't have time to think about it. Meanwhile, watch out for the pretenders. They're out to use you. They may even perform miracles. But if they claim to be me, or from me, don't believe them."

Many of us think that if anyone ever earned the right to be called the Messiah, it was Jesus. But I know many of you will be thinking, "I don't buy that stuff about Mark being historically accurate. I still think it was all a fairy tale. There probably never was a Jesus, and he certainly wasn't the messiah." Fair enough. But then, if Jesus wasn't the messiah, neither is anyone who claims to be his second coming. So watch out for people like Moon.

To answer Raevmo's question, I know that the Rev. Moon is a false messiah because Jesus said he was. I know Moon is a false messiah because he's out for fame, wealth, and power. If there ever was a messiah, it was Jesus. And if he returns, he said it would be clear as lightning.

Monkeys Give a Hoot notes the folllowing:

"Watch out!" It's a simple phrase, but researchers have long debated whether nonhuman primates use something like it. A new study indicates that they do: Even when not threatened themselves, African blue monkeys warn neighbors of nearby predators. However, some skeptics maintain that the animals are acting out of fear, not concern for others.

The short article about monkey alarms concludes with this paragraph:

But Gregory Radick, a science historian who writes on primate language at the University of Leeds, U.K., finds the study's conclusions worth considering. He notes that although the monkey could be motivated by fear, it's still adjusting its alarm based on the threat that's posed to others. The jury may be out for quite some time, he says. "This kind of experiment is not easy to interpret, … and that leaves room for other people to throw some doubt on the experiment's meaning."

Experimental results are not always easy to interpret. Sometimes interpretations can be multiple and the choice among them dictated by prevailing ideas. The amino acid chirality mystery shows how scientific data can be interpreted. From the blog entry:

So the mystery is reduced to that of why at some point in time there were many more L amino acids than the R form. It has been shown that amino acids can form spontaneously from inorganic materias under some conditions (the Miller-Urey experiments demonstrated this.) However, one would expect equal amounts of R and L amino acids under such circumstances.

Experimental evidence indicates earthly conditions give rise to racemic amino acid mixtures. If life originated on earth, as a consequence of dysteleological chemical reactions, one would expect a preponderence of L amino acids- the opposite of what is suggested by the evidence. So how is this to be interpreted? There are several options. We could have interpreted the data as indicating that the dysteleological assumption is wrong. Sure. Fat chance bub. Or we could adopt the old OOL standby and interpret the evidence as indicating the data is incomplete. Eventually new data will show that generating unbalanced amino acid mixtures on earth really was feasible. Then there is the third option. Amino acids came to earth from extra-terrestrial sources. That interpretation currently holds the favored ground. Why? Another quote:

But there's another way out, because we know that in fact amino acids can form in interstellar space, since they were found in parts of the Murchison meteorite (and later others) that were uncontaminated with Earthly material. Furthermore, there's one definite way that amino acids which existed originally in an equal mixture of L and R forms on a chunk of rock hurtling through space could have their proportion tilted in one direction or the other:

The theoretical means by which unequal amounts of left and right-handed amino acids could have resulted is discussed. There are primary interpretations and secondary interpretations and both types are laden with assumptions. Amino acids can be degraded as well as generated. How long would an imbalance persist if newly generated amino acids on earth are of equal amounts? How long do theoretical models indicate it would take to utilize amino acids within arising life forms? Finally, how plausible and detailed are such models?

When you read the inevitable criticism of design concepts, which incorporate a science sez template, distinguish between beliefs predicated on interpretations of data and the data itself.

A structural engineer has been reviewing Mike Gene's book, The Design Matrix; a Consilience of Clues, and has recently discussed Behe's concept of Irreducible Complexity, and how Mike Gene views it in his book, here.

Behe Starts a Furor

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.”
Michael Behe, Chapter 2, Darwin’s Black Box

In 1996, Dr. Michael Behe provided in his book, Darwin’s Black Box (DBB), this simple definition for a simple, yet potentially powerful concept – irreducible complexity (IC). In the subsequent years, an academic war of words broke out which beckoned the question: why the furor? Surely the above definition alone couldn’t have started the maelstrom of criticisms that began soon after it was published?

Let me propose that much of the hullaballoo (did I really just write hullaballoo???) is due to Behe’s application of IC, which amounts to IC = evolution impossible. To clarify Behe’s argument, while it is impossible for a direct evolutionary pathway to produce an IC system, it is possible for indirect evolutionary pathways to do so. However, when he scanned the scientific literature, Behe noted that there was no paper describing the indirect routes in significant detail.

The Traditional Template Invoked

The concept IC as defined by Michael Behe is simple, brilliant and stands as a potential marker of design. To provide backup, Behe eloquently presented several cases of IC systems (cilia, flagellum, blood clotting, etc.). He also anticipated most of the criticisms directed towards his thesis and answered them fairly adequately. However, Behe became entangled within the Tradition Template of the debate the moment he presented a negative argument (IC = evolution impossible), and even though Behe attempts to make a positive argument for design in Chapters 8 through 11, the negative argument dominates DBB. In my opinion, this tactic has halted the concept of IC in its tracks before teleologists could take it for a proper test drive. By arguing an impossibility, Behe unwittingly assumed the “traditional role” of the dissenter.

Accordingly, Behe’s critics were more than willing to assume their “traditional role” to demonstrate that it is possible for DE to produce IC systems. Kenneth Miller, a biologist at Brown University, is generally credited with proposing the best argument against Behe’s application of IC: cooption* - the parts of an IC system were coopted from parts of other precursor systems. With cooption, Miller showed it was possible for evolutionary mechanisms to develop IC systems (Note I said possible, not plausible nor probable). Since Behe is arguing it is impossible for evolution to produce an IC system, all Miller had to do was show it was merely possible. Thus it would appear that the Traditional Template has given a seemingly crushing blow to IC**.

Hopping Down the Bunny Trail

Enter Mike Gene. In his book, The Design Matrix (DM), Gene takes IC for a test drive within the Explanatory Continuum.

First, Gene pointed out that cooption was “really the only evolutionary explanation that has the potential to explain the origin of an [IC] system.” Second, he recognised a flaw in the cooption argument:

“The most basic problem with the conventional use of [cooption] is its complete reliance on chance.”
Mike Gene, Chapter 8, The Design Matrix

Third, Gene made the cooption explanation plausible by incorporating his working front-loaded evolution*** (FLE) hypothesis.

Mike Gene then applied the brakes and headed back to the starting line. He granted that cooption is possible, thus avoids getting entangled in the Traditional. Gene then investigated what independent evidence is needed to progress it to plausible.

If cooption was to be a viable explanation, it must be gradual. Then Mike Gene pointed out that to construct an IC system through gradual cooption, “the previous existence of simpler precursors and multiplied functions” should be abundant. If these precursors are missing, then the IC system can be said to consist of “system-dependent parts”.

“A system-dependent part would be something that does not exist or function apart from the context of the machine.”
Mike Gene, Chapter 8, The Design Matrix

With this, Mike Gene laid the framework for one of four criteria in his Design Matrix (more on this in the next post). This, coupled with FLE, has advanced IC from Behe’s simple yet powerful concept to a possible marker of design. Thanks to Mike Gene, IC has new life.

Lawrence Gage explores the Four Levels of Teleology in some depth. What are often referred to as atelic phenomenon do in fact satisfy teleology at some levels. By breaking down teleology into distinct steps, Gage suggests a process perspective which would restore teleology to its once occupied perch.

Paley's watch met the four levels of teleology but Paley's critics have sucessfully argued that nature has shown itself capable of engendering ever increasing biological complexity through blind forces of nature. Richard Dawkins and others have used the blind metaphor like an atelic mascot. An historic shift yielding an atelic paradigm. The study of nature yields knowledge. Assume what you wish about teleology.

At this point it is worth recalling that atelic assumptions are operative, and not a validation of the actual nature of the forces studied. Labeling evolution an atelic process does not make it atelic. The watch may run once it exists but forces of nature have not revealed how it was put together. Neither do we understand how it was wound up. Organisms maintain their complexity and replicate by means of a capacity to consume material and extract energy from it. Reproductive fidelity is a distinguishing feature of living organisms.

Intelligent design critics believe atelic operative assumptions will yet reveal life's mysteries. Perhaps. Gage writes:

Similarly, notice that each of Artigas's levels of teleology is at a greater remove from the subject of the telos. The end of a process is simply part of the process. The goal of a tendency is a future part of regular process. A value for a subject is hypothetical or possible future part of a process. The purpose of a plan is possible future part of an intelligent subject's activity.

If life is the end process and prior purpose evidenced by physical discontinuities, then goals of cellular replication and adaptation would be enabled by intelligent activity. If that were the case the search for atelic processes is a vain endeavor.

For Dawkins and like-minded thinkers the order evident in the universe and natural laws just exist. It's just the way things are. Teleology is mainly confined to effects induced by humans. Yet to the brute intelligence of lower organisms even such obvious teleology can remain hidden. They are not able to grasp the process levels apparent to more intelligent humans. Yet humans may be no different. Like brutes in a field they may simply be unable to connect the dots that unfolded from purposeful plan to end process.

A website named X-Ray Technician Schools [Alabama] has offered its "Top 100 Cutting-Edge Science Blogs" list, and Telic Thoughts weighs in at #35, #2 under the Biology section. After General, Astronomy, Academic, Research and Group Blogs. Had they started with Biology, we'd be much farther up the list.

Seed's ScienceBlogs comes in collectively at #32 under Group Blogs, none are individually singled out. Panda's Thumb appears at #84 under Miscellaneous.

Now, this list isn't exactly authoritative for the blogosphere ratings system (that has long held PZ's Pharyngula as the #1 Science Blog despite its piddly percentage of actual science posts). But it is a pretty good collection of blogs about this and that, and NOT dominated by Seed's insular empire of professional Culture Warriors. Check it out!

Dear Prof. Dembski,

[I've added a little, in bold type] I'm writing this letter out of a sincere concern that I have had for some time. I haven't written it up until now, because I didn't think it was quite suitable material for TelicThoughts. We usually try to focus on science and the question of intelligent design, and this is more about religion. Specifically, about Jonathan Wells' religion. A number of years ago, way back at ARN, it was revealed that Dr. Wells was a member of the Unification Church. This meant that he believed that the Reverend Sun Myung Moon was the second coming of Jesus Christ. I was shocked to learn it at the time. But I figured, what the heck? We all have our quirky idiosyncratic beliefs. Why shouldn't he?

But I've become more concerned by a few recent events. First, you co-authored a recent book with Dr. Wells. Second, Dr. Wells had a role in the recent movie, Expelled, where he offered a definition of evolution that would be acceptable to any Young Earth Creationist. Third, you recently had a thread at your own blog where you accused Darwin of purposely trying to be the messiah of a secular religion. Fourth, I've recently been told that we should hold fellow Christians to a higher standard than we do non-Christians.

So I'm asking that you distance yourself from Dr. Wells' religion, and publicly declare that the Reverend Moon is a false messiah. If you are willing to make such a declaration against Darwin (a view that many Christians would dispute), you should at the very least make an equally strong declaration against the Reverend Moon. If you refuse to do this, I will suspect [Of course, I often have delusional suspicions. For example, when Mike Gene's book was late coming out, I suspected that he was pulling our leg the whole time. And I still suspect that Bush/Cheney/Pentagon at least deliberately allowed 9/11. So let the reader take my suspicions with a large grain of salt] that either you also believe in the Reverend Moon, or that either you or the Discovery Institute might suffer monetary loss by making such a declaration.

This letter is not intended as a criticism of your views on Intelligent Design, or of the work you have done in this field. I have stated on a number of occasions that I greatly admire your work. If you need to know my real name, Mike Gene has my permission to give it to you.

Sincerely,
Bilbo

P.S. To fellow TTers, I promise not to bring this subject up again. And if any of you think this letter is inappropriate, you have my permission to delete it.

The search for life beyond earth continues. NASA Now Looking for Life's Building Blocks on Mars has this to say:

Phoenix scientists announced yesterday that the mission finally confirmed the presence of subsurface water ice in the north polar regions of Mars — first detected by NASA's Mars Odyssey orbiter in 2002 — about two months after touching down on the Martian surface on May 25.

The lander is now analyzing the ice to see if it was ever a liquid and if it contains organic materials, the building blocks of life.

Among the indicators of possible life water is basic. Yet water alone may not suffice even with hospitable atmospheric conditions and temperatures. Time will tell. More from the linked article:

The evidence available to scientists now suggests that Mars could have harbored life, it's just a matter of finding a spot that preserves the signs of it, he added. And Phoenix's landing site, or even MSL's, may not be the ideal spot to go and look for those signs, whether by sending another rover or staging a mission to return a sample to Earth.

There are plenty of other environments on Mars where Jakosky would like to look for signs of life. While he can't point to a particular spot, there is evidence that Mars once had features that could have supported life, including ancient lake beds, ancient highlands where evidence suggests that water existed for long periods of time, and hot springs — "places like Yellowstone," as Jakosky describes them.

Some scientists, such as Seelos, doubt that clear evidence of Martian life itself will ever be found because any life would have likely been microbial, which is not easily preserved as fossils. But Jakosky sees this as an "unnecessarily pessimistic" view, because ancient microbes have been preserved in some places on Earth.

Conditions vary greatly throughout the universe but if life arose on earth because the environment favored chemical reactions that lead to cells, then we have an expectation that similar environments likewise give rise to those results.

Why is it that those who borrow 99% of their ideas from Plato, Augustine and Aquinas are "sheep"…

while those who borrow 99% of their ideas from Nietzsche, Marx and Freud are "free thinkers"?

Let's get back to biology. The latest from Mike Gene's blog:

[Caveman ask that somebody do that magic thing with links]

Setting up a culture of cells is a relatively simple task. All you need is some media, which would be a solution that contains all the ingredients needed for cell growth, and some cells, obtained from another previous culture. Put simply, you fill a container with media and add a small amount of cells. These cells then do what cells do – they divide and form a large population of cells over time. In other words, the machinery within the cells converts the simple biomolecules in the media into new cells.

But now I have a puzzle for you.

Lets begin by making a media with the following ingredients: amino acids, glucose, vitamins, nucleosides, salts and citrate. Next, let’s transfer a single Tetrahymena cell to 1 microliter of the media. That corresponds to a density of 1000 cells per ml. What happens? The cell does what cells do – it divides and forms a population of cells.

But what happens if you transfer a single Tetrahymena cell to 10 microliters of media (which corresponds of 100 cells per mi.)? Answer – it dies.

So why does this single-celled organism die when it is surrounded by an abundance of food and there are no predators or toxins around?

I’ll give ya the answer in the next entry.

Or does anybody here know the answer?

For people who want to discuss the question of what Jesus claimed about himself. I changed the title from "Open Thread" to the above, to avoid confusion with Joy's "Open Thread."

Discussion on the lengthy Remarkable Nucleotides thread has become unwieldy, as well as not much about remarkable nucleotides anymore. This thread serves for continuing sidelines off-topic there - OoL and ET scenarios primarily, as well as physical diversions.

My questioning post:

John, Bradford, TP & Zach have engaged the possibility of life being ubiquitous in the universe over in the Remarkable Nucleotides thread I am unable to follow or post to. So I'm putting my question to them here.

I previously mentioned in a somewhat light tone that there are a lot of humans - including astronauts from the Mercury, Gemini and Apollo missions - who claim to have encountered sentient extraterrestrial beings. I also mentioned the fact that these ETs are described as "humanoid" in form. And that it's not impossible to think of a scenario for an alien civilization to have designed and front-loaded the first cells on this planet just to see how the evolutionary tape would replay in this environment. It resulted in the appearance (after a mere ~600 million years) of sentient, intelligent "humanoids."

Yes, I know that single-celled life has been here for around 3.8 billion years. It just didn't reach a level of cooperative complexity that enabled the appearance of specialized information processing and sensory structures until the early Cambrian. At which point life 'exploded' in a veritable orgy of creative expression of genes that had been present all along. All forms of complex life that evolved from that Golden Age of creative excess have come and/or gone between then and now.

I suspect Hameroff is correct in his theoretical extrapolation to that event in the history of life on planet earth as being triggered by the development of sufficient information processing structures to cross the threshold from simple awareness to actual functional consciousness. A quantitative measure, a scientific hypothesis that makes a lot of conceptual sense and could explain a lot that blind, accidental, agent-less evolution simply cannot explain.

Once consciousness enters the causal realm of the Prime Directive, it obviously drives an evolutionary engine that is rather amazingly swift and efficient. There's a big difference between 600 million and 3.8 billion years. A 3.2 billion year difference. Once creativity exploded, it exploded big time and things happened really, really fast. Relatively speaking.

If we were to find that humanoid ETs were involved, it would suggest that humanoid life forms are (one of) the inevitable results of biological evolution under the guidance of increasing quantitative expression of consciousness. That increasing sentience (self-awareness) and intelligence (learning, problem-solving) is inevitable to at least one line of the possible forms front-loaded into the global genome.

Q: Can it be agreed that quantitative expression of the physical mechanisms of consciousness is likely to be a telic aspect of life's evolution toward increasing complexity (organic/ecological 'loopiness' and adaptive behaviors)?

Q: Can we agree that a sufficient concentration of those mechanisms may enable a causal role (interfacing with the environment) for consciousness in shifting evolution into overdrive (after 3.2 billion years of relative quietude)?

Q: Can we agree that causal (and telic, toward expression of itself) consciousness playing a role in relatively rapid adaptive evolution qualifies as "Intelligent Design?"
________

TP's Response:

You asked…

Q: Can it be agreed that quantitative expression of the physical mechanisms of consciousness is likely to be a telic aspect of life's evolution toward increasing complexity (organic/ecological 'loopiness' and adaptive form/behaviors)?

My version is to suggest that, at the very least, our telic universe has an apparent purpose of existing and being consistent with itself.

Such a universe will literally move heaven and Earth to make happen whatever needs to in order to fulfill its purpose.

I don't find it overly difficult to imagine that life is necessary to fulfill this kind of universe's purpose.

I have intentionally used terms and concepts that are a compromise between the two standard dueling metaphysical positions. You asked "Can it be agreed that…" Highly doubtful, but I am interested to see.

Q: Can we agree that a sufficient concentration of those mechanisms may enable a causal role (interfacing with the environment) for consciousness in shifting evolution into overdrive (after 3.2 billion years of relative quietude)?

Once we get past the first part, this should be easy (famous last words).

Q: Can we agree that causal (and telic, toward expression of itself) consciousness playing a role in relatively rapid adaptive evolution qualifies as "Intelligent Design?"

I still would prefer "Conscious Design" or "Telic Design" but that is old news.

Yep. That's the headline. Whole thing reads…

Biology Enters 'The Matrix' Through New Computer Language

Bradford posted about a Protein Folding Game, where scientists are hoping humans turn out to be more efficient than computer modeling programs have been at functional folding. This article is about a new computer language that can mimic the 'mind' of a cell.

Yep. You read that right. Enter "Little b," working off an AI programming language called LISP…

"LISP isn't like typical programs, it's more like a conversation," says Gunawardena. "When we input data into Little b, Little b responds to it and reasons over the data."

For example, Gunawardena's lab works on kinases, a kind of protein that transfers phosphate chemicals to other proteins in order to regulate their activity. While this property is common to all kinases, there is a great deal of variety in how particular kinases carry this out. Little b, however, understands this basic property of kinases, this abstraction.

Little b promises to model complex protein folding, molecular machine construction (with function built-in) and complex biochemical interactions.

"This language is stepping into an unknown universe, when your computer starts building things for you," says Gunawardena. "Your whole relationship with the computer becomes a different one. You've ceded some control to the machine. The machine is drawing inferences on your behalf and constructing things for you."

So. The question seems obvious to me. If you design a machine that designs, and it in turn informs you that indeed the designs are designed, will the Darwinian die-hards believe it?

"The success of Darwin's theory…stems from the manner in which Darwin's theory has been successfully used to guide research and generate insights into biology. Such research and insights have, in turn, generated much circumstancial evidence that supports the Darwinian thesis." (Mike Gene in his book, The Design Matrix; a Consilience of Clues, p.26).

"Could we please dispense with any patronizing nonsense about Darwin being less than the messiah of a materialistic religion that pretends to find its justification in science. If Darwin was not the alpha and omega of evolution, then he was either a knave or a fool or a madman. Darwin did not leave us any other options. He did not intend to." (William Dembski, Uncommon Descent,)
http://www.uncommondescent.com/evolution/olivia-judson-lets-not-call-w hat-were-doing-darwinism/

http://www.uncommondescent.com/evolution/olivia-judson-lets-not-call-w hat-were-doing-darwinism/
http://www.uncommondescent.com/evolution/olivia-judson-lets-not-call-w hat-were-doing-darwinism

Good thing Mike left when he did, or we would have to stone him (no, not the Bob Dylan kind of stone, Uncle Rock).

For the benefit of any Theistic Evolutionists that might be lurking amongst us. Or any just plain ol' Darwinists.

Interesting…when I first posted the link to Dembski's article, it worked just fine. Now there's a space between the 'w' and 'hat', which produces an error. And I can't seem to be able to fix it. Wonder how that happened. Couldn't be Dave Scot could it?