The Limits of Adaptability

Dave, I'm sure some of your detractors will take that as permission to call you a prick all the time now. ;)

You say that almost like they needed either permission or added incentive... :-) -ds Patrick

Hello Dave,
What do you percieve to be the role of the environment over the course of geological time in the playing out of LUCA's front-loaded phylogeny? As I see it, you could argue that: 1) the environment plays no role in the preprogrammed course of evolution; 2) the LUCA genome was sufficiently plastic to allow for the adaptation of some descendents to extreme environmental changes; 3) events in the physical evolution of the earth itself were anticipated in the design of LUCA's genome.

Thanks

I think a better question is what was the role of life in shaping the environment. Early life oxygenated the atmosphere which paved the way for fast metabolisms of multi-cellular life and with the oxygen came the ozone layer which blocks harmful ultraviolet radiation making it possible for life to move from the water to the land. Life continues to pump carbon dioxide into the atmosphere creating a greenhouse gas blanket which prevents a snowball earth from becoming permanently established as the sun's output has diminished significantly over geologic time, the heat of the earth's formation has escaped, and radioactive elements that help keep the earth warm by their decay have diminished in quantity. One might also go a step further and speculate that life layed down vast petroleum reserves for a specific reason - so that life could have an energy source for industrialization. Looking to the future, one might presume that the ultimate goal of life on this planet is to reproduce and transport itself to a younger planet and start the cycle all over again. The transport would require a technological civilization able to send artificial spacecraft to new solar systems. In fact the spacecraft "Voyager" just recently exited our solar system. It would be surprising if some microbial spores didn't hitch a ride on it. The ability to locate suitable young planets also requires industrialization to build telescopes big enough to resolve earth-size planets around other stars and use spectral analysis to determine their makeup. In point of fact the next generation of giant telescopes should be able to do just that - it's the hottest area in astronomy today. I just finished reading an article about the latest generation of telescopes in SciAm. You have to subscribe for the full article but these behemoths have planned construction costs north of $1 billion and up to 10 years to fabricate all the adaptive optics. Consider the entire biosphere as a single organism. Its goal, like all organisms, is to reproduce and get its progeny to fertile ground so they may prosper. Like all organisms, the planetary organism will devote whatever resources are necessary to reproduce as, like anything else, it is going to die whether it reproduces or not. The only question is whether it manages to reproduce before dying. In that view, the human species becomes the planetary organism's reproductive organ. We're like the fluff on a dandelion seed which enables transport of the seed to fertile new ground, only in this case the transport is across light years of vacuum. So if someone calls me a big prick I take it as a compliment as being a big prick is really the purpose of our species - a prick big enough to deliver seed across light years of empty space. -ds

Michael Tuite

Chris Hyland

Here's the problem for me, Chris. I'm a computer hardware/software design engineer and have a lot of experience in factory automation. So I gravitate towards the programmable protein assembling machinery (DNA/ribosome) as the thing I want explained because 1) I understand the architecture of robotic assemblers and 2) the machine is present in every living thing and is programmed using virtually identical digital code and 3) it is probably the most complex machine in a cell. If its origin can be demonstrated with reasonable certainty to be possible absent intelligent agency then I'll concede everything else that follows after it requires no intelligent agency.

But here's the nut. If design isn't ruled out prior to the appearance of the first DNA based cell then one cannot rule out the possibility that the first cell contained a very complex genome that was designed to diversify along a preprogrammed path much as a fertilized human egg cell diversifies into myriad specialized cell types, tissue types, and organs. I coined a term for a hypothetical LUCA with a front-loaded genome - a phylogenetic stem cell. A front-loaded evolution, which by definition must be designed, fits all the empirical data as near as I can tell. The best objection is that genetic information that isn't under selection pressure can't be preserved long enough to be passed down intact over billions of years. However, that's nonsense and anyone that knows anything about information processing in modern computers knows that there are many ways to preserve data with any level of required fidelity over any number of copy and store iterations. There are FAR more complex things happening at the molecular level inside cells than simple error detection and it's certainly not a problem for a designer capable of creating the system to incorporate the necessary algorithms to protect critical data against copy errors for as long as they need such protection.

DaveScot

"This seems to be more of an origin of life problem than an evolution problem." Quite true. As I said before, ID is perfectly compatible with many modern conceptions of evolution. It's pretty much just the synthetic theory that it has problems with. I think that the problem is that there are more biologists who hold religiously to the synthetic theory than you may realize. But yes, there is nothing in ID which specifically states that there had to be continuous intervention. Many in the ID community think that there was only one intervention event -- at the origin of life. The point is that at some point a symbolic coding system and specified information had to arise, and the only known cause of those two things that we know of are intelligent beings. The main difference that ID brings into evolutionary theory is that information generally comes from a larger pool of information, not a smaller one. While non-ID evolutionary biologists believe that information builds up from non-information, ID'ers think that information either specializes, degrades, or stays the same. Therefore, current information probably came from a _larger_ pool of information, not a smaller one. In addition, for the origin of life, if you assume that the origin came about by non-Darwinian means, then you get a vastly different conception of early life. Much of the conceptions of universal common ancestry come from a specific point of view of the origin-of-life. For example, if we did not hold to the Darwinian conception of the origin of life, what evidence is there that the different phyla had common ancestors? All we have is a (putative) time sequence, which do not show ancestry, nor even evidence of ancestry (I say putative, because, being a Creationist myself, I hold to the fossil record having a cause in physics [the flood] rather than time). In fact, even secular views of the origin-of-life, if not viewed in the Darwinian model, have this same problem. For an overview of the situation, see my blog post about Gordon Malcon's essay on Monophyly: http://crevobits.blogspot.com/2006/02/monophyly-in-biology.html So, the two theoretical differences that ID bring to the table are: 1) The origin-of-life (which, as I've pointed out, DOES have more impact on evolutionary thought than most evolutionists admit) 2) That information specializes out of larger pools, it does not build up from smaller pools [except on a very limitted basis, and even those are questionable. The theoretical limit for a single jump in information is a step 500 bits long. Still, I would personally consider this specialization rather than actually information-adding.] A major practical difference that ID brings to the table is that viewing systems from a historical perspective may not be as useful as viewing them from a holistic perspective. This is the essence of Jonathan Wells' work on Centrioles, Behe/Minnich's work on the flagellum, and to a much, much, much, much, much, much lesser extent, my own work on the immune system. I have an essay that talks a bit about information change from a computer programming perspective, if you are interested: http://www.issuesthatmatter.com/genomicchange1.html The part that may interest you starts with the heading "The Nature of Computational Systems and Programs". Other than that, ID has no real conflict with modern evolutionary theory. It's the Darwinian Fundamentalists who have a problem with it, because of its implications (there needing to be a source for the information). Also, there are a number of people against ID because the Darwinian Fundamentalist propoganda has convinced them that ID is something that it is not. The same thing happens with Creationism, with the exception that at least some of what is said about Creationism is true :) [defensible, I think, but true nonetheless] johnnyb

"So the question is, where did all this information come from? More importantly, can a symbolic coding system even begin to develop on its own? The answer that the Darwinists have is to simply push Darwinism back further in the pipeline. “Yes, these are not Darwinistic mechanisms, but there is no reason to think that they can’t be produced by Darwinian mechanisms” is what they’ll say. But is that true? The fact is, Darwinism has not been any help at all in determining how these guided change processes came into being. And, optimization theory indicates that it won’t be able to." This seems to be more of an origin of life problem than an evolution problem. When thinking about evolution I have to assume some information is already present, but I make no assumptions about where that information comes from. People talk about LUCA, as a hypothetical starting point, but no one expects this to be the first life form. I know this will be an unaceptable position to people, but we just don't have enough information about the origin of life. Chris Hyland

I wrote: “Throw in the fact that the SCNT could only happen in the presence of intelligent agents” Chris Hyland asks: How is this again sorry? SCNT requires living enucleated mammalian eggs which are then fed somatic cells. Only humans working in laboratories (intelligent agents) can bring this experiment about; hence the most reasonable assumption is that the cell's cytoplasm has this latent potential within it (and one could add, this came about 'outside the reach' of NS). PaV

"This would be unfortunate, and scientists should be doing more to change it, but a really fail to see what this has to do with intelligent design. Sure there are questions with the modern synthesis, but evo-devo, phenotypic plasticity, epigenesis etc are answering these questions." Also remember directed mutagenesis. This is a good question, and it deserves answering. I think the issue is is that all of these processes require a pre-established repository of information to work. The "beauty" of neo-Darwinism to those that held it, was that it purported to offer a change process that did not require _any_ existing information in the genome to work. What all of these new ideas within biology are saying, however, is that all of these change mechanisms that we are discovering require already existing information in order to proceed properly. Evo-devo requires that the different pathways which are switched on and off already be there in order to be available to be switched on and off. Adaptive mutagenesis requires that the organism includes information about which changes are potentially useful and which ones are not. So the question is, where did all this information come from? More importantly, can a symbolic coding system even begin to develop on its own? The answer that the Darwinists have is to simply push Darwinism back further in the pipeline. "Yes, these are not Darwinistic mechanisms, but there is no reason to think that they can't be produced by Darwinian mechanisms" is what they'll say. But is that true? The fact is, Darwinism has not been any help at all in determining how these guided change processes came into being. And, optimization theory indicates that it won't be able to. See the following for information on that: http://www.4truth.net/site/apps/nl/content3.asp?c=hiKXLbPNLrF&b=784461&ct=1742245 http://www.designinference.com/documents/2005.03.Searching_Large_Spaces.pdf The only model available which deals with presently-acting causes is intelligent design. We humans are able to create information systems as intelligent designers. In fact, intelligent agents are the _only_ known cause for producing symbolic systems. See Albert Voie's paper: http://home.online.no/~albvoie/index.cfm The model of evolution currently favored by ID'ers is probably this one: http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html The model of evolution currently favored by Creationists is probably this one: http://www.grisda.org/origins/54005.pdf [by the way, if you live near Dayton, Ohio, you should come out to Cedarville University on June 5th-9th for a Creationism Research conference -- see what such people are actually talking about -- http://www.bryancore.org/bsg/ ] Anyway, let me know if I failed to fully explain something. Oh, just to point out, one of the things that is rarely brought up in the ID debate, but is of central importance, is whether or not intelligent agency is distinct from (though limitted by) material causes. A lot of evolutionists discount ID because they don't believe in any other kinds of causes than material causes -- intelligent causes are simply complex combinations of material causes. ID has a view of causation where intelligent causes, while limitted by material circumstances, are of a different kind of cause than material causes. To a materialist, there is only chance and necessity. To an ID'er, there is chance, necessity, and agency -- all interdependent and interacting, but fundamentally different in their natures. johnnyb

"When people refer to “Darwinism” they are referring to the synthetic theory. It is not necessarily true that they are referring to the modern theory of evolution (different people have different conceptions of what this is). That is what the PT-people want you to think. “Darwinism” specifically refers to RM+NS as the primary cause of organismal form. This is still how evolution is presented to the public, despite the fact that this is not what biologists are actually working with." When I go home to visit the folks next week, I am going to have a flick through my old science books to see exactly what I was taught, I have also asked them to get a copy of a current textbook from my school. I suspect that what is taught could be very different from what I regard to be the modern theory of evolution. This would be unfortunate, and scientists should be doing more to change it, but a really fail to see what this has to do with intelligent design. Sure there are questions with the modern synthesis, but evo-devo, phenotypic plasticity, epigenesis etc are answering these questions. Chris Hyland

"I am assuming that when people say ‘Darwinism’ they are referring to the modern theory of evolution. Please correct me if I’m wrong." When people refer to "Darwinism" they are referring to the synthetic theory. It is not necessarily true that they are referring to the modern theory of evolution (different people have different conceptions of what this is). That is what the PT-people want you to think. "Darwinism" specifically refers to RM+NS as the primary cause of organismal form. This is still how evolution is presented to the public, despite the fact that this is not what biologists are actually working with. More generally, "Darwinism"'s central idea is that all genetic change occurs without respect to organismal fitness. This is what "teach the controversy" is about -- telling people that this model of evolution is not the only valid one, and in fact there are serious problems with it. Any somatic feedback to the germ line is incompatile with neo-Darwinism. Any guiding to focus mutations on adaptive changes is incompatible with neo-Darwinism. Phillip Johnson has a great lecture on this. Instead of "Darwinism" he refers to the "Blind Watchmaker Hypothesis" which is essentially the same thing. http://www.uctv.tv/library-test.asp?showID=6444 The idea that ID is against all modern evolutionary theory is simply an attempt to paint ID as the "bad guy" for science. It has no real basis in the truth. johnnyb

Adaptationalism at least provides sufficient content to the label "Darwinian Evolution" for the concept to be criticized at any level in principle. jaredl

dickatkinson: "All these references to the adaptation (or pre-adaptation, exadaptation, etc) of ORGANISMS is off the point. It is implicitly Lamarckian." Not really. Larmarckianism is the idea that traits can be acquired during the organism's lifespan (depending on what they're exposed to) and these traits can subsequently be inherited. To a limited extent (retroviruses,epigenetic modifications, genetic assimilation in microbes, etc) lamarkian inheritance has been demonstrated *in principle*. Personally, I don't like using the term because these examples are not entirely analogous with what Lamark originally proposed. But to each their own. In either case, simply discussing how an organism's physiology might respond to diverse and/or completely novel environments is not explicitly or implicitly Larmarkian. The level of biochemistry complexity does pose some interesting questions for evolution and ID, but I see that as no reason to ignore the interaction of the entire organismal phenotype with the environment. A lot of interesting and meaningful stuff goes on at the organismal level that can not be appreciated from the biochemical level. One of these things, which was the subject of the original thread as I understood it, was the observed flexibility of organisms in the face of changing and/or completely novel environments. Unless you're a microbiologist, focusing exclusively on the biochemistry here would be a bit myopic. Also, I'd like to avoid discussing "pre-adaptation" as well. It is a bad term and has largely been dispensed with in the evo. community. It's teleologically loaded and implies evolution can forsee what is to come. In the modern scientific formulation it can not. The term has been replaced with "exaptation," which indicates that a trait that was either a) selected previously for some other reason or b) present for no adaptive reason and, in virtue of some change in the environmental or genetic landscape, it subsequently became functional. Finally, I think it is very unfortunate that a preponderance of the pro-evolution pundits appear to be of the adaptationalist (darwinian fundamentalist) mindset. In my experience, these people--typically, but not exclusively, from England--have become largely irrelevant in the active research community. (at least the molecularly oriented community) That is probably why they have more time to take on ID in public forums. Unfortunately, they have helped shaped the minds of what many individuals believe evolutionary theory to be. No one in their right mind, in my opinion, is arguing that every response of an organism to "whatever" in an environment is *adaptively* selected for and evolved to be there. The more interesting question is the engineering question. Given the organism, what are its environmental tolerance parameters and are these consistent with darwinian evolution? great_ape

Just what is the selection advantage for inverting the visual input from the eye anyway? Let's say we have this newly evolved eye attached to a neural net, the brain. Saying a "neural net based vision system would be able to right a flipped image quite readily" isn't an answer. It's not a question of capability, it's a question of why would this neural net want to solve this problem (or even recognize it as such) in the first place. How does the neural net know that the visual input is upside-down and needs to be corrected on the fly? We know this isn't a hardwired solution, but when we wear those vision-inverting goggles how does the brain recognize the image as being upside-down? If you've ever been to a children's science museum you may have run into one of those games where you're required to trace a path while viewing a maze through a mirror. It may take a couple minutes but eventually you'll get used to working backwards. If an organism is born with inverted vision it'd learn to mesh the sensory input from its body with that from its eyes; that'd be its "normal" state of being. Would living with one's vision being upside down harm an organism's survivability? How does evolving the ability to correct the inversion increase an organism's survivability? Patrick

I am assuming that when people say 'Darwinism' they are referring to the modern theory of evolution. Please correct me if I'm wrong. Chris Hyland

What is in direct odds with Darwinism? Chris Hyland

"In the sense that mutations will tend to fix the new phenotype after a certain number of generations? I agree that genetic assimilation is involved in evolution, so do a great deal of evolutionary biologists." And there is a great deal in evolutionary biology that is in direct agreement with both Creationism and Intelligent Design, and at odds with Darwinism. It's just that evolutionary biologists have trouble admitting this fact. johnnyb

All these references to the adaptation (or pre-adaptation, exadaptation, etc) of ORGANISMS is off the point. It is implicitly Lamarckian. Both mutation and selection are biochemical processes, and it at the biochemical level that they are most problematic. Richard Dawkins, for example, conveniently switches to the organism level when the biochemical challenge is tricky. (Apart, that is, from his disastrous "Methinks it is a weasel" argument.) It is as if one were to argue that a Model-T "just" evolved into a Mondeo, without reference to the design stage, R&D, production technology and so on. Much more of a problem is deciding which is the appropriate level to locate the "intelligence" of Intelligent Design. Is it anywhere in the reductionist spectrum of physics-chemistry-biochemistry-biology, or off the scale at one or other end, or "somewhere else" (in which case, what can "somewhere else" even mean?) The modern Christian view, a kind of Slow Creationism (which might unkindly be called The Little Whimper in contrast to The Big Bang), has a serious conceptual flaw. A truly omnipotent God would not need to create all those staphylococci, insects, nematodes and the like. If His aim was to make human beings, He picked a particularly wasteful method. Of course you could just say that human beings should not attempt to understand the Almighty: "He moves in a mysterious way." But that is not dissimilar to the attitude of Galileo's inquisitors, who simply refused to look through the telescope. dickatkinson dickatkinson

bFast, Great Ape, et. al., We keep talking about "ultimate survivability", "come what may", etc., as though "general survivability" is some kind of evolutionarily selectable trait. I don't think it is or can be. Nothing survives generally, only particularly, and survival requires a balance of traits suited to particular environments. Take bFast's examples of extreme cold, floods and forest fires. A killer whale will do very well in the first two but very poorly in the last. A sparrow will do well in the latter two but have trouble with the first. And it is the very traits that make the killer whale survivable in the the first two that make it vulnerable to the last. Same with the bird. The light weight and low body fat that permit it to fly, and so survive floods and forest fires, make it less survivable in extreme cold. Survival is always a tradeoff between traits. There is no such thing as "general survivability". As an analogy, there is no such thing as a "generally great" major league baseball player. A player who can pitch 80 mph, hit .200, play a little catcher, is a mediocre shortstop, an OK center fielder, and play a little first base, will rarely make the major leagues. The player who can't hit at all or field anywhere, but can pitch 95 mph will make it over the first player everytime. Similarly, a player who can't pitch at all, can't play catcher or shortstop, but can hit .330 with 45 HRs/year, will get paid big dollars. That's because baseball players don't play a "position in general", they usually play one particular position or a small set of positions. They need to be very good at a couple things, not mediocre at a whole lot of things. Similarly, organisms do not live in environments-in-general. They live in a few particular environments, and evolution will select for survival in those, not for survivability-in-general. Cheers, Dave T. taciturnus

"Throw in the fact that the SCNT could only happen in the presence of intelligent agents" How is this again sorry? "I agree that this is the correct in the light of evolution, however I think what’s really being questioned the unlimited genetic flexibility." What has unlimited genetic flexibility? "While I agree that development does affect morphology to a great deal, I also want to suggest that perhaps genetic assimilation (which you alluded to, but did not name earlier) may be a directed mechanism for genomic change. " In the sense that mutations will tend to fix the new phenotype after a certain number of generations? I agree that genetic assimilation is involved in evolution, so do a great deal of evolutionary biologists. Chris Hyland

@ great_ape "In that case, the sub-optimal (for this particular short-term environment) yet ultimately more robust/flexible genetic makeup will survive over the long-term" I agree that this is the correct in the light of evolution, however I think what's really being questioned the unlimited genetic flexibility. I personally, don't like the reverse prism cerebellar adjustment argument, but I like the main point of that arguement. Evolution is schizophrenic, b/c in its easy to come up w/ any mumbo jumbo story about a specific ie flexibility of the cerebellum and b/c its evolved so much reverse prisms are essentially solvable problem, although the organism never encountered that in nature, but the it switches gears to generally ascribe genetic flexibility to almost ALL FACETS of an organism giving it the benefit of the doubt. This is something totally different, one RM + NS is not accounting for, yet I see time and time again. Example: Today CNN reported that Harvard and MIT have completed their first round of comparison of the genome of humans and monkeys and conjectured divergence 6.3 million years ago. They were looking mostly at mating compatability (according to the article) to make their decisions. Using mating as their (the scientists) tool, they believe several lines were isolated, came back after a couple of millenia and started mating again. It's easy to make these kind of conjectures looking via tunnel vision at just one trait (mating wouldn't be a "trait" per se but you get what I mean). Instead of this, I'd really like to see how during the "mating" RM + NS how, phonation, posture, hairless bodies, silent ovulation, psychology, molecular changes of the sperm and ovum, etc. were all evolving at the "same time" w/ just RM + NS, to the specificity it shows today. Note, if you say preferential mating took care of all those things, you're gonna run into the same if not bigger prbs... jpark320

Dave T.: "Differential survival in a particular environment, or series of environments, spreads traits that promote survival in those environments, not a generalized tendency to survival (which I think is an empty concept anyway, evolutionarily speaking)." The point Dave T. mentioned above should be carefully considered. He is correct that evolution, at least in its modern formulation, is extremely short-sighted. It's not sighted at all, in fact. If an organism were to find itself in an very static environment (i.e. no noise in the system) over a long period of time, it would presumably LOCK onto that environment genetically and possibly be ill-equipped to endure serious pertubations in the future. If, on the other hand, the environment was always subject to some degree of pertubation, the locking may never occur. In that case, the sub-optimal (for this particular short-term environment) yet ultimately more robust/flexible genetic makeup will survive over the long-term. Consider a 3-D adaptive landscape. There's a really high peak representing super-fitness for a given environment. But it's also a steep peak. Being on top certainly has its advantages, but if the wind of change blows and the landscape shifts slightly, it's very easy to fall off such a peak. Sure if the wind never blew, a population may eventually wander onto that peak, lock onto it, and find itself in a a rather precarious situation genetically/phenotypically. But if the wind does blow from time to time, and the adaptive landscape trembles and shifts a bit, it's best to be on a wide mound. Maybe it's not as high, but it's a lot harder to fall off. great_ape

"A somatic cell has the the same genome as a cell that will develop into an egg cell." This is not entirely true. Some somatic cells undergo specialized recombination events which modify the genome for that tissue. V(D)J recombination is the prime example. johnnyb

Heh, the insecure atheistic simpletons over at MZ Peyers blog are having a field day with this one. Lot's of remarks about Dr. D's "bad math", complete with links to obscure sites which attempt to refute said math with bogus explanations that demonstrate a failure in understanding the relevant math in the first place. Good times, gotta love it. :)

Scott

(I pressed the wrong key, and, presto, up went the post. I'll continue now. Sorry.) Anyone who's worked with computers knows that if your BIOS goes bad, you're dead in the water. It would appear that the 'cell' plays the same part in the biosphere that 'hardware' plays in information-processing machines. I think it is John Davison who says (or quotes someone as saying) that everything living comes from an egg. The proverbial taunt for Darwinists is: "What came first, the chicken, or the egg?" This SCNT seems to strongly suggest that the answer is the 'egg.' Taking all this a step further, scientists are now talking about heritable epigenetic 'markers', and an 'epigenetic code.' If, indeed, such a 'code' exists, then its existence intimates that a 'code' exists, over and above that of the genome, that 'directs' the processing of the genome (after all, the enucleated egg 'reprogrammed' the inserted genomic material). It would seem that this would be the far more elemental and important code. And its presence brings into question, at least some extent, the whole notion of RM, in that it would be easy to postulate that this more fundamental 'epigenetic code' simply reprograms the existent DNA, and what appears to be 'random' is, in actual fact, a 'programmed response.' Throw in the fact that the SCNT could only happen in the presence of intelligent agents--and hence, outside the reach of NS, while not completely dismantling NDE, it makes a very powerful argument for teleology: ie, the mammalian egg is going to become an embryo come what may----just as everything tends to its end. PaV

Perhaps I can take the discussion back to an earlier point--epigenesis.

What the SCNT (somatic cell nuclear transfer) seem to demonstrate is epigenesis to the n-th degree. The cytoplasm is directing the nuclear material. To me, the critical language is this: "The “headless” (no nucleus, no genome, etc.) egg cell proceeds to break down/destroy the non-nucleic parts of the somatic cell. It then “gets ahold of” the somatic nucleus. It then proceeds to “reprogram” the nucleus to express the appropriate genes for embryonic life."

What's critical is the "reprogram"-ing part. A somatic cell has the the same genome as a cell that will develop into an egg cell. The difference between the two cells is what part of the genome is being activated and expressed. This experiment seems to strongly suggest that it is the 'cell' (cytoplasm) that is more critical, more fundamental to life than even the DNA.

It is rather natural to compare the genome to a 'program'. But we all know that 'software' has to have a 'hardware' component. Even in PC's, your computer wouldn't boot up if you didn't have a BIOS

BIOS is technically called firmware - neither software nor hardware. My main responsibility at Dell was laptop BIOS programming. In more modern BIOS stored in reprogrammable FLASH ROM there's a protected (in hardware) FLASH segment that never gets reprogrammed and its sole function in life is to load a new main BIOS in the happenstance that the existing one is somehow corrupted. Nature probably has a similar mechanism and SCNT might be exposing it. It seems that for everything humans invent nature has an antecedent. -ds PaV

Chris -- While I agree that development does affect morphology to a great deal, I also want to suggest that perhaps genetic assimilation (which you alluded to, but did not name earlier) may be a directed mechanism for genomic change. You might be interested in my comments on Scott Gilbert's work: http://baraminology.blogspot.com/2006/02/new-science-of-eco-devo.html I've also summarized another relevant review article here: http://baraminology.blogspot.com/2006/04/genetic-assimilation-and-directional.html But the really important thing I wanted to point out was Sternberg's hypothesis of teleomorphic recursivity: http://www.annalsnyas.org/cgi/content/abstract/901/1/224 We have generally been studying genomes in one direction only. Perhaps it is time to view genomes and form as mutually modifying each other. johnnyb

Hey, that's the ticket! I'm starting to think like a genUINE Darwinist now! Let me at some of that research money. es58

no problem for darwinism, it explains everything, so, at some point, it evolved "generic shortterm adaptability" because who can think of a more necessary requirement than that (except where it doesn't have it of course, in which case, it wasn't necessary there,don't you see?) presto chango! es58

"Let me suggest that every time there is a particular environmental surprise, the creatures that happen to have an allele mix which is particularly suited to that surprise will survive better than those who don’t" Changes in morphology in response to environmental change have little to to do with allele frequencies, it's to do with development. Because the developmental cycle relies in part on the environmental conditions, if the condidtions are different then the cycle may be altered without any genetic change. That is, patterns of gene expression that affect development are altered. Chris Hyland

Tiax: It’s suggested that babies see things upside down for the first few days, until their brains adjust to the need to flip things. If a baby’s brain can make that adjustment, I suspect my brain could handle the task just as well. If a baby’s brain can make that adjustment, I suspect my brain could handle the task just as well. Don’t flatter yourself. I’d put the odds at 50/50. -ds Ds, having studied child psychology on the masters level, I have seen evidence that the former -- babies seeing upside down -- does seem to be a documented phenomenon. (Sorry, can't put my hands on it.) As those who have been studied with inverting glasses all seem to have developed the ability to naturally correct for the circomstance, I seen no reason to believe that Tiax would not as well. Tiax may not be as quick at it as a baby is, but that's hardly the point, is it. bFast

Dave T.:"Differential survival in a particular environment, or series of environments, spreads traits that promote survival in those environments, not a generalized tendency to survival" Let me suggest that every time there is a particular environmental surprise, the creatures that happen to have an allele mix which is particularly suited to that surprise will survive better than those who don't, but the creatures who happen to have a "tonacity" mix, a "come what may" mix will also survive better than the "average". (I would suggest that in each surprise event, the "particularly suiteds" will do better than the "come what mays".) In the case that "environmental surprises" are each significantly different, I would suggest that the tonacity mix, being favored above par in each event, will rise above the mix that is ideally suited for each surprise. If a "come what may" gene is possible, then the "come what may" gene will do very well indeed. bFast

Chris -- This paper contains research on many examples of cellular RNA that wound up in Retroviruses: http://intl.rnajournal.org/cgi/content/abstract/10/2/299 This book contains evidences that variable-region genes are transported to germ cells via RNA: http://www.amazon.com/gp/product/0738201715/104-5426795-6513569?v=glance&n=283155 If you search pubmed on the author's names you can find several of the papers they wrote. Unfortunately, my ILL loan period expired before I got to finish the book, and I haven't had a chance to get the papers yet, either. But the first paper mentioned above is a free download. johnnyb

bFast, Thinking critically is just what I am trying to do, perhaps not successfully. I don't understand the point of your comments about sub-freezing temperatures, forest fires, and flooding. I understand why each of those conditions would cause some creatures to survive and not others. In particular, those creatures that are well-adapted for cold-weather will survive the low temperatures, those that can handle smoke will survive the forest fires, and those that can swim will survive the flood. I can understand how each of those circumstances would cause the survival trait to persist and eventually dominate in a population. What I don't understand is how surviving cold-weather leads to the spread of a general trait of surviving "whatever", in particular, surviving environmental circumstances the species has not yet experienced. Why does surviving the cold weather spread traits that not only help it survive cold weather, but survive forest fires and floods as well? Or are you saying that a particular animal suffered the cold weather, the forest fire, and the flood? Then it survives not because it is adapted to "whatever", but because it is particularly adapted to cold weather, forest fires and floods. But such adaptation says nothing about how the animal would survive in a desert or a tornado. To support the claim that animals survive that are adapted to "whatever", it needs to be shown that survival in a particular circumstance, or series of circumstances, leads to traits that allow it to survive in circumstances unrelated to that particular animal's experience. The animal that survives the flood but never experiences a forest fire somehow becomes adapted to survival in a forest fire... and cold temperatures, tornadoes, earthquakes, meteor strikes, and "whatever" else might conceivably happen. That is the step I question. Differential survival in a particular environment, or series of environments, spreads traits that promote survival in those environments, not a generalized tendency to survival (which I think is an empty concept anyway, evolutionarily speaking). Cheers, Dave T. taciturnus

"Retroviruses are able to pack up somatic DNA and transport it to germ cells." Oh I misread that, do you have a link to a paper on this, thanks. Chris Hyland

"Chris – Epigenetics is not the only way for heritable somatic changes. Retroviruses are viewed by some as an implementation of Lamarckism. Retroviruses are able to pack up somatic DNA and transport it to germ cells. There is some evidence for this occurring in the variable regions of antibody genes, as well as other places. " I know, my point was that if these things are not part of 'Darwinism' then Darwinism isn't synonymous with the modern theory of evolution. Chris Hyland

Well, I'd put it another way. I have yet to see any credible alternative to Intelligent Design--period! There's science and then there's pure wild speculation that can become science. In my opinion Darwin never made the cut. Rude

I don't know if this is a good line of argumentation or not. However, what makes me think, at least at first blush, that there might be something to it is to look at PZ Meyer's reaction: http://scienceblogs.com/pharyngula/2006/05/its_called_development_mr_demb.php His fundamental point is this: "This is absurd. Basically what Dembski is arguing here is that if organisms are not absolutely rigid and inflexible in their development, incapable of responding to variation in their environment, then evolution is wrong. He ignores (or more likely, is completely unaware of) everything we've known about basic developmental biology for a century and a half—the concept of regulation seems likely to freak poor Bill Dembski out, and I fear the mention of the words evo-devo and eco-devo would cause his head to ka-splode" Meyers does not say ANYTHING about why or how Darwinian evolution could produce such mechanisms. All he says is that because developmental biology knows about it, it cannot be contradictory of Darwinism. Read it again, because it can be easily missed. In fact, what the argument is is that such developmental enhancements cannot be the _product_ of Darwinian evolution. PZ Meyer's ONLY DEFENSE in this case is to say that such things exist. But that is just the point! He is agreeing with Dembski that they exist. Somehow he thinks that their mere existance makes it evidence of Darwinism's ability to do such a thing. This is classical Darwinian thinking. Because structure X exists, and because we already know that Darwinian evolution is true, then structure X cannot ever be used as an argument against Darwinian evolution, because it was produced by it. So the best reaction PZ can come up with is not "let me tell you how Darwinism can produce such functions" but rather "these functions can obviously be produced by Darwinism because they exist". Chris -- Epigenetics is not the only way for heritable somatic changes. Retroviruses are viewed by some as an implementation of Lamarckism. Retroviruses are able to pack up somatic DNA and transport it to germ cells. There is some evidence for this occurring in the variable regions of antibody genes, as well as other places. johnnyb

I have yet to see any credible alternative to Darwinian Fundamentalism aside from intelligent design. jaredl

Nobody says it better, Rude... you said with great clarity what I was trying to say before. It is so beautiful the way looking at the evolution of language, the human form of "word", can yield such insight! Interestingly, the color range blue-violet is associated with the pineal and crown chakras, which are said to be associated with wisdom and insight from higher spheres, whereas the color red is associated with the ground or root chakra, associated with the physical body and its connection to earth. tinabrewer

From the peanut gallery again: In our civilization's past animate life was conceived as tripartite—spirit and soul and body [το πνευμα και η ψυχη και το σωμα] for example in 1Thess 5:23, with bone and flesh [עֶצֶם וּבָשָׂר] standing for body throughout the Torah as for example in Genesis 2:23. Everywhere spirit is associated with understanding and truth (i.e., information), and soul is associated with desire and agency. I have been surprised to find the same tripartite conception of the person among indigenous people. For example along the Columbia River there is even an association with color: waq'íšwit 'breath' is associated with words and the color blue, tmná 'heart' is associated with intention and the color red, and wáwnakwšaš 'body' is associated with the color yellow (or white)—"red, white and blue" was Stephen Meyer's quick response. If this is our natural intuition, then science should be open to at least the possibility of all three: information (spirit) be it Platonic or informatio ex nihilo, agency (soul) from whatever source, and mechanism (body). Why should EVERYTHING reduce to just one of these? A reductionism blind to a large portion of our intuition just might turn out to be a little too reductionist. Rude

Dave T: "The difficulty is that organisms are never faced with “whatever.” They are always faced with a particular environment for which a particular set of biological features promote survival." You don't live the same life I live, I guess. I don't live in a single, generally static, environment. On a wicked day, the temperature outside is -60. (I live in the Canadian sub-arctic.) This makes little difference to me with my thermostatically controlled heat, but to the animals who live outside, it is survival time. Periodically the air is filled with smoke because of a forest fire. It makes little difference to me, but to the animals in the burning forest, it is survival time. Once in a while we have a hefty rain storm, and flooding. For the animals living outside, it is survival time. When a couple of feet of snow dump down, for the animals who live outside it is survival time. The environment is not static. The environment is not static by any means within the lifespan of individual animals. Animals with the best "come what may" survival mechanisms have a distinct selectable advantage. Read my posts, I am a true IDer, I just am unwilling to get too excited by the next hypothesis that comes along. We've got to think critically, or the other guys will do it for us. bFast

"Lamarck was probably right all along about acquired characters being heritable." There are several methods of epigenetic inheritance, which technically is Lamarckian, that can result in evolution that does not involve changes in the genome sequence. "What’s to discuss? Systems which are preadapted to unforseen and unforseeable contingencies seem to discredit the blind watchmaker hypothesis, which seems to imply that any feature of a living system is, in essence, the minimal feature necessary to secure reproductive success over competitors." Most evolutionary biologists I know don't hold to adaptationism, which says that every feature of an organism must be an adaptation shaped by natural selection. Stephen Jay Gould called it 'Darwinian Fundamentalism'. "There are marine organisms that change the shape of their shells if they’re thrust into different water chemistries…New parameters to the physiological equation yield different results. The question is this: is it shocking that many of these results will be *viable* and functional results. There is a body of literature on a process called cannalization, which I think is relevant to this discussion." It appears that in many cases this 'deveopmental plasticity' arises from the properties of the developmental network. What is quite interesting is that if a species is forced to exhibit a new phenotype in response to some environmental condition, after a certain number of generations this then becomes the 'default' phenotype even if the condition is removed. So the RM comes after the NS. Chris Hyland

bFast, You wrote: "Living organisms experience the unforseen all of the time, the ones best able to deal with “whatever” would survive the best." The difficulty is that organisms are never faced with "whatever." They are always faced with a particular environment for which a particular set of biological features promote survival. NDE selects for those features, not a set of features that promotes survival in a general sense, or that might provide survivability in some novel environmental circumstance not yet experienced. In any case, to explain the origin of a species in terms of its ability to survive "whatever" is really to give up on a Darwinian explanation altogether. The driving force of NDE is differential survival and its effect on the structure and development of life. Changing environments across space and time are supposed to account for the enormous variety and peculiarity of life as we find it, because different organisms have varying rates of survival in different environments. If now we explain a species, not in terms of the particular environmental history it has experienced, but in terms of its ability to survive "whatever", then its evolutionary history is irrelevant and the explanation is not Darwinian. In fact, such an explanation would have to be teleological. Cheers, Dave T. taciturnus

It boils down to the main mechanism of neo-Darwinism: wishful thinking. geoffrobinson

jaredl: forget that snippet! Pushed the wrong button. more later. tinabrewer

jaredl: while the body definitely functions in an apparently mechanistic way, there are ce tinabrewer

When I put my NDE hat on, I am totally unsurprised at the "flip glasses" phenomenon. In general, being able to deal with unforseen situations is very selectable, as far as I can see. Living organisms experience the unforseen all of the time, the ones best able to deal with "whatever" would survive the best. We know that neural networks are very operative in the brain. In AI we have been trying to replicate the technology for years. A feature of neural networks is that they learn from their experience. A neural net based vision system would be able to right a flipped image quite redily. The egg thing sounds much more challenging. I wonder, however, if there isn't a very simple explanation. We know that mammal sperm uses a flagellum to find the egg. Therefore mammal sperm has "baggage" hanging off of the nucleus. Could it be that the egg has proteins which are designed to strip the sperm down to its nucleus? If so, could this protein act as a general organic material stripper with the sense only of the nucleus wall, where it ceases to act? If this were so, and such would be a simple solution to ridding the sperm of its flagellum, then the above description is no longer that surprising. While I am always into a good challenge for NDE, I am not so sure that this is the one. bFast

One of the big "whys" I at which I always thought evolution failed miserably in trying to address was "was why is their biodiversity in the same habitat?" One would think that if fitness was the goal of natural selection everything that came from the first cell would have evolved to the same thing. Or considering bacteria exists everywhere, why bother evolving? tribune7

thanks again Rude! The movement toward vitalism is alive and well, thank goodness. Sheldrake does make very interesting points. I think he extrapolates too far from what he is able to show experimentally, but his ideas definitely point to a non-material component of life which would end up endorsing a more Lamarckian type of evolutionary theory. tinabrewer

The ability to adapt appears mechanistic in operation here - that's why I say that such adaptability does not provide evidence of a vitalistic component in the systems under consideration. We needn't appeal to some vitalistic force to explain immune responses to synthetic compounds, for example, and that's the class of systems we're looking at here. jaredl

Oh boy! Hadn't read 3 above! It had said what I just said before I said it. Sorry. Rude

TinaB - Perhaps "preadapted" was a bad word to use in this context. I mean that a system with an inherent ability to adapt to the contingencies mentioned (while not necessarily supplying evidence of a vitalistic component to the system in question) does supply evidence against the blind watchmaker hypothesis simply because it requires purposeful gullibility to believe that such a capacity was the minimal response required in the immediate environment to secure reproductive success. jaredl

Just a wild idea here from the peanut gallery: If organisms do prove to be more adaptable than can be explained by the mechanism of the organism, then maybe it's time to reconsider the old vitalism. This, of course, is what Rupert Sheldrake is all about and, yes, we're probably wise to maintain a bit of distance what with the New Ageyness of that movement. But Sheldrake does make interesting reading which just might inspire some alert young mind out there in a remote corner of ID. One gets a hint here and there that life really doesn't bootstrap up entirely from the DNA within the cell but rather there must be some direction from outside. Rude

It seems that adaptablility is something Darwinism could never explain even in principle. The engine that drives Darwinian evolution is differential survival. An organism, through RM or some other means, obtains an attribute that allows it a better chance of survival in its environment. It therefore leaves more offspring and, eventually, the new attribute spreads throughout the population. Implicit in the scenario is the assumption that competing organisms do not adapt to the crisis. They follow the script and exit stage left so the new, improved model can take over. Death and extinction are just as critical to the story as survival and reproduction, and to the extent that something adapts and survives to the new circumstances in a way other than RM+NS, it's not following a part authorized by the Darwinian playbill. The Kettleworth moths, for example, only show natural selection at work because the light colored moths don't adapt and instead allow themselves to be eaten when the soot darkens the trees (I know from "Icons of Evolution" that there are a lot of problems with the moth story. The point is, even taken at face value, the Darwinian case depends on the light moths not adapting to the new circumstances.) Adaptablility, defined as the power to change in the face of unforeseen circumstances in a way that enhances survival, is a quality that cannot be explained by Darwinian evolution because the core concept of differential survival requires non-adaptability. Cheers, Dave T. taciturnus

This discussion reminds me of a heated argument in an undergrad class of mine. Upon hearing mention of a discovery linking a certain gene to predisposition for alcoholism, a young woman stands up and says this is all nonsense. "Human genes evolved during a time when there was no such thing as alcohol!!" Therefore there could be no such thing as a gene for alcoholism.
Teleological language can result in confusion. The fact is when you put a complex organism in a completely novel/artificial scenario you just don't know what is going to happen a priori given its genetic complement. Many times it fails or exhibits some nonoptimal response. Sometimes its current complement of genetics/physiology allows it to adapt. There are marine organisms that change the shape of their shells if they're thrust into different water chemistries...New parameters to the physiological equation yield different results. The question is this: is it shocking that many of these results will be *viable* and functional results. There is a body of literature on a process called cannalization, which I think is relevant to this discussion. Certain systems appear to be inherrently flexible. An example would be the layout of blood vessels in your body. We've all seen the pictures of tumors re-routing capillaries to feed them. Part of the reason they are able to do this is b/c of the built-in flexibility. One would expect a certain degree of robustness in many systems to be present in evolved organisms. As we all know, absolute rigidity is seldom a successful strategy. When is the flexibility observed so excessive that it's impossible to occur outside of design? Again, very hard to say, and it ultimately brings us back to the design inference biocomplexity question. But to claim that it, without additional analysis, such examples refute darwinian evolution seems premature.

I'm taking you off the moderation list. Your comments will henceforward appear immediately. Don't make me regret it. -ds great_ape

I would say that the systems aren't "preadapted", but that a more organic way of viewing it is that life has an inherent quality of active adaptability. This inherent quality, in my view, stems from a substance or essence of living things which is non-material. In homeopathic medicine, for example, this governing intelligence is called "vital force". All of the tools of science are made up of matter, and are therefore at best able to measure the material effects of this non-material living substance. The problem comes in when it is assumed that EVERYTHING has its originating cause IN MATTER. Then, things (like design, rapid adaptability) which bear the clear earmarks of a living intelligence, must be ignored, repudiated, or reduced to matter. tinabrewer

What's to discuss? Systems which are preadapted to unforseen and unforseeable contingencies seem to discredit the blind watchmaker hypothesis, which seems to imply that any feature of a living system is, in essence, the minimal feature necessary to secure reproductive success over competitors. That being the case, it is literally incredible that the minimal requirements for reproductive success just happens to be preadaptation to situations which only arise from modern human technological intervention. jaredl

"For example, we’ve all heard of the experiments where human subjects wear goggles that flip their visual experience upside down. After some period of time the brain/mind/soul flips things upright. Since never in evolutionary history could anything of that sort ever occurred on a sufficiently regular or long-term basis to give rise to that ability, that ability alone shows that Darwinian evolution is a false (incomplete) theory."

That experiment just goes to show the flexibility of the brain, which is explicable in terms of Darwinian evolution. Adaptability itself is a trait that natural selection can favor.

There are more extreme examples of this in nature. Experiments have shown (see links below) that some species of bacteria actually increase their rates of mutation in times of hardship, which makes it more likely for colonies to adapt before they die off completely.

http://rhosgobel.blogspot.com/2005/05/antibiotic-resistance-in-bacteria.html
http://newsinfo.iu.edu/news/page/normal/1160.html

They also exchange genes with other bacteria to spread the wealth, so to speak. Turning up the mutation rate of certain genes involved in toxin resistance in response to stress is something that was blogged about here a year ago. It's probably not rare or extreme. Anything a lowly e.coli can do shouldn't be an ability any more complex organisms have in their toolbox. Indeed, one should presume that more complex organisms have even more complex survival tools at their disposal. Lamarck was probably right all along about acquired characters being heritable. He certainly was for prokaryotes and anything a prokaryote can do I expect their ostensible descendents the eukaryotes can do even better. What's extreme is thinking we have more than a small inkling of what's really going on with evolution and the machinery of life. Clinging to the simple random mutation & natural selection dogma is naive and nothing more than a palliative to assure ourselves that we have a good understanding of what's happening and are just missing some details. It's also a security blanket for chance worshipping atheists that dominate certain echelons of the science establishment and we all know how hard it is to get a small child to give up her blanky. The whole premise that random mutation and natural selection are the drivers of creative evolution has become a lame duck. -ds wb4

I keep bees and one of the amazing things that they do (among many !) is that one can introduce a new queen and, if the correct precautions are made, the hive will "adopt" her as their own. Why do they do this ?

This also reminds me of grafting trees together. How can one tree tolerate being grafted to another ?

I think the answer lies in robustness. Natural selection will act for organisms to be robust - especially to the environment (I mean, look at the tremendously diverse environmental conditions a 1000 year old tree must contend with - drought, fire, herbivory). This robustness may lead to the accomodation of weird, unnatural circumastances.

I mean, we do OK living in the suburbs. How weird and unnatural is that ?

As I recall honeybees are the only species besides humans that have a symbolic language. Workers that find a rich food source can return to the hive and symbolically communicate directions to other workers on how to navigate to it. bdelloid

Dr. Dembski Sir, a speculative argument on my part... In reference to the enucleated cell portion of your article, is it possible for me to argue with you that it has never happened? No, not very well, but I say this, I think it happened on one occasion or something like it. At any rate, it is something for me to think about... carbon14atom

I'm not too convinced about the vision flipping thing. The brain already flips what's coming in, since the retina sends it an upside-down image. Shouldn't our minds be able to just apply the flip again when things aren't coming out right-side up? It's suggested that babies see things upside down for the first few days, until their brains adjust to the need to flip things. If a baby's brain can make that adjustment, I suspect my brain could handle the task just as well.

If a baby's brain can make that adjustment, I suspect my brain could handle the task just as well. Don't flatter yourself. I'd put the odds at 50/50. -ds Tiax