Flagella - Real and Fictional

I'm amazed that they still cling to the bacterial flagellum.

"A fanatic is one who can’t change his mind and won’t change the subject.

- Winston Churchill

Would love to hear or view the debate with between you and Behe. Is there a link anywhere?

without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Perakh’s point that illustrations of flagella look more artificial, more “designed,” than actual flagella is well-taken. A pity that to get to it, one must wade through his plodding, wordy attack on Bessette’s claim that the existence of theistic Great Scientists of ages past and of an alleged 40% theism rate among modern US scientists is “inconvenient” for atheists. A silly claim, true, but Perakh is capable of equal silliness. He rears up at Bessette’s claim to know what atheists are thinking --

“How could Bessette know that atheists indeed construe his two facts (assuming they are true) as ‘inconvenient’? Has he conducted a poll of the atheistic scientists?”

-- but then goes into a mind-reading act of his own, a few lines later:

“ . . . those 40% of contemporary [theistic] scientists in the USA . . . overwhelmingly inherited their faith from their parents and adhere to it throughout their lives because of having emotionally absorbed it in their childhood.”

Since turnabout is fair play, how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

I doubt he has. What I think is that a double standard has just flashed. I think that to Perakh all religion is utterly absurd by definition, so it is simply self-evident that any scientist who professes religious belief must do so “because of having emotionally absorbed it in their childhood.” Just as, apparently, when Bessette would like to think that atheists find certain facts “inconvenient,” no evidence is necessary for him, either.

The level of discourse here is, let’s say, lower than it might be. Perakh emits a strong whiff of that true-believer funk so often emitted by those who have decided that Religion Is the Enemy and that they, themselves, are the true Warriors of Light.

LG

Perhaps it's fraud, or perhaps it's merely the fact that IDologists, not being scientists in spirit, do not have any motivation to dig deeper when they see something that appears to support their agenda.

Severino wrote: "Would love to hear or view the debate with between you and Behe. Is there a link anywhere?"
To my knowledge, no links are available. If somebody is indeed very much interested in that debate, perhaps a DVD could be requested from Larry Kane's program. However, the arrangements I described made the debate of a rather limited interest as I had no way to adequately respond to Behe whose posters I did not see, nor himself or the moderator. It was about 30 min long, with several commercial breaks, so not much could be discussed anyway. My position has been explained in detail more than once (for example see my post here or those posts referred as [20, 21, 22} in this article, or in chapter 2 of my book Unintelligent Design.

arent these the same people who are always complaining about haeckel diagrams?

I appreciate time and effort Larry Gilman has put into his comment. Yes, Larry, like Bessette, I did not conduct a survey of scientists, I just evinced my opinion with which you are free to disagree.

If Larry Gilman objects to making statements not based on a thorough investigation, why did he resort in a similar fashion to stating an opinion of my attitude to religion? If he wanted to know my view of religion, rather than asuming what it is, based on just one sentence relating to that question in passing, he could have looked up my essays dealing in a more detailed way with that topic, some of which are posted on Talk Reason in the pertinent section. I regret that Larry Gilman does not like the parts of my article dealing with religious scientists. I guess having perused my more detailed essays on that topic, he still would not like my views, but it can't be helped. I don't mind learning about Larry Gilman's views being contrary to those of mine, but hopefully I am entitled to my own views as well. Ironic (or rather condescending) statements about delusional self-confidence of supposed "Warriors of Light" while testifying to Larry's sense of humor, are hardly convincing.

snex said: arent these the same people who are always complaining about haeckel diagrams?

I think that this shows that the flagellum really is a perfect mascot of ID.
More so and in more ways than I think they intend though...

And of course even did flagella "look like a machines," such would be irrelevant to whether they were evolved structures. ("Looking like a machine" is an awfully underspecified property.) So the argument's a fraud times two.

how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

Religious conversion by adults is itself a fascinating topic. I wonder if some qualified person has ever explored it in depth.

Behe has often referred to the bacterial flagellum as the equivalent of an outboard motor. However, his analogy is flawed because the "motor" that turns the flagellum is INSIDE of the cell wall of the bacterium. The proper analogy would be to a boat with an inboard motor that powers a propeller that is outside of the boat's hull. (In the case of a jet drive, the motor and propeller may both be inside of the boat's hull.)

Scott Beach said: Behe has often referred to the bacterial flagellum as the equivalent of an outboard motor. However, his analogy is flawed because the "motor" that turns the flagellum is INSIDE of the cell wall of the bacterium. The proper analogy would be to a boat with an inboard motor that powers a propeller that is outside of the boat’s hull.

Religious conversion by adults is itself a fascinating topic. I wonder if some qualified person has ever explored it in depth.

This study also looks interesting. Thanks.

Even the images in Perakh's essay somewhat overstate the "machine-like" aspects of flagellar structure, because these are idealized optimized structures, most of them presented at the somewhat abstracted level of ribbon diagrams, with all of the subunits in identical conformations. If one has never seen molecular dynamics simulations, it is easy to think of these as rigid parts, rather than molecules with a huge number of rotatable bonds in constant Brownian motion, looking not so much like an engine as like a shaken Jello dessert.

Obligatory post kudos - it is a good topic.

As the peppered moth illustrations were mentioned, in my layman opinion I suspect the photographs tells us very little about the real structural behavior of the flagellum.

The fixation process is rapid freeze cryogenic for a reason, resolution problems abound, and in a sense it is giving as much or more of a false impression to show electron microscopy for persons untrained in the differences to light photography than an idealized sketch. (Not that this heavily referenced Talk Reason article should be expected to do so.)

IMHO what would be really impressive would be to show an animation of proteins being pushed about in the cellular environment, stochastically working through a mechanic function while going through any possible conformation changes they may have. Or at least taking the idealized structure diagrams of figure 5-7 and randomize distances and angles in and between molecules according to a freeze frame of the real distribution.

Data comparing man made "macromachine" and micromachine tolerances and work cycle efficiency with biochemical machines would also be telling.

Meanwhile EM pictures is a great antidote for claims of perfection.

Btw, Bessette's argument from authority seems even sillier to me than mentioned here. If it had any value at all, it would be that the trend has been for more scientists being or becoming atheists, especially among the great authorities I believe.

But as it has no relevance for the discussed science outside of what motivates ID advocates attacking it, these statistics are best forgotten. Practically it is a problem for me if a paper is written in french, not if it is written by a buddist. [Disclaimer for french readers: I'm a language agnostic, and "freedom for language" is no problem for me - but I haven't absorbed french in my childhood.]

oops, trrll was faster on the images and simulation.

wow whining about overstated flagellum complexity. and like the NCSE made clear it only took four mutations to make the eye(didn't hear anyone blogging that oversimplification). everything is simple, the cell is so simple! time and frothy bubbles concentrating....compacting and wham!! simple. wait the frothy bubbles had to mutate! simple happens all the time(although never observed). Observation, that isn't a necessary step in the scientific process is it? Repitition? who needs it? so simple indeed.

Mark Perakh said: let me ask Larry Gilman a question: Can you predict, with an overwhelming probability, what the religious affiliation will be of a boy born today in Islamabad?

isiyouthgroup@hotmail.com said: like the NCSE made clear it only took four mutations to make the eye

Observation, that isn't a necessary step in the scientific process is it? Repitition? who needs it?

what was that movie that Behe and expelled allegedly stole from? the one about the cell?

Torbjorn: you are a man of precision. Have you ever researched this mutation bizzo? I have heard - and I have every reason to believe it to be true - that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable. I know for a fact that our genetics are getting worse. So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

Do common descent advocates get around this by hypothesizing a different world in the past, or do they simply ignore the facts? And have you got anything authoritative on the rate of genetic damage?

Philip Bruce Heywood said: I have heard...that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable.

Philip Bruce Heywood said: I know for a fact that our genetics are getting worse.

Philip Bruce Heywood said: So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

[Perakh] rears up at Bessette’s claim to know what atheists are thinking – “How could Bessette know that atheists indeed construe his two facts (assuming they are true) as ‘inconvenient’? Has he conducted a poll of the atheistic scientists?” – but then goes into a mind-reading act of his own, a few lines later: “ … those 40% of contemporary [theistic] scientists in the USA … overwhelmingly inherited their faith from their parents and adhere to it throughout their lives because of having emotionally absorbed it in their childhood.” Since turnabout is fair play, how does Perakh know that continued adherence to some form of religious belief is causally explained across the whole group of US theistic scientists by their “having emotionally absorbed it in their childhood”? How does he rule out a contribution from mature mental and emotional processes to ongoing religiosity, possibly including reason, volition, and adult religious experience? To paraphrase his own question, has he conducted a poll of the theistic scientists?

— Larry Gilman

Some comments on the whole 40% thing. First of all, this statistic is used by TEs such as Collins and myself to let lay people know that evolutionary biology is not some atheistic plot. Atheistic scientists aren't really the audience here. Also, last time I checked 40% is not a majority and it also refers to generic theists and not particular faiths. Another interesting thing is that a similar survey at the beginning of the 20th Century showed the same 40/60 split between theist/atheist. So, despite all that has happened in the last 100 years this hasn't moved. So much for the self-serving conspiracy theories of ID or the New Atheists.

Let me show you the use of this statistic in its context. For example, Collins used this statistic in the AAAS video on YouTube which is a response to Expelled to show that Evolution was not *necessarily* atheistic. (Actually a pre-response because the video was shot long before the movie.) The NAS in their statement on evolution and creationism also noted this. The bottom line here is scientists who believe Evolution and believe in God exist and not that we are some sort of majority. N.B. my use of prepositions in my previous sentence.

One book that was not reviewed that also dealt with this statistic was The Reason for God by an evangelical pastor and theologian by the name of Tim Keller. He had an interesting and in my opinion on target interpretation of the statistic. Neither side is going away. We are neither moving to a "godless nation" nor to a "theocracy". I guess we will just need to learn to live with each other.

trrll said: Even the images in Perakh's essay somewhat overstate the "machine-like" aspects of flagellar structure, because these are idealized optimized structures, most of them presented at the somewhat abstracted level of ribbon diagrams, with all of the subunits in identical conformations. If one has never seen molecular dynamics simulations, it is easy to think of these as rigid parts, rather than molecules with a huge number of rotatable bonds in constant Brownian motion, looking not so much like an engine as like a shaken Jello dessert.

Bobby said: Perhaps it's fraud, or perhaps it's merely the fact that IDologists, not being scientists in spirit, do not have any motivation to dig deeper when they see something that appears to support their agenda.

neo-anti-luddite said:

Philip Bruce Heywood said: I have heard...that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable.

Why?

Philip Bruce Heywood said: I know for a fact that our genetics are getting worse.

How do you know that "for a fact"? What evidence do you have to support this claim?

Philip Bruce Heywood said: So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

Why?

Mark Perakh says: “that the images of flagella they endlessly demonstrate are heavily doctored, and that the real observed flagella do not look like “machines” at all.”

.

Wow, they don’t actually look like man-made machines? Amazing. Still, function over form fellow that I am, I tend to be a bit more impressed by function than by form. And let’s face it, flagella function is rather impressive, especially for those of us who believe that it’s all the miraculous result of random mutations and selection . . . but then I suppose with an infinite number of organisms and time, all things, including flagella and sentient beings, are not only possible, they’re inevitable.

but then I suppose with an infinite number of organisms and time, all things, including flagella and sentient beings, are not only possible, they’re inevitable.

Philip Bruce Heywood said: Torbjorn: you are a man of precision. Have you ever researched this mutation bizzo? I have heard - and I have every reason to believe it to be true - that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man

if it continues, will ultimately render higher life inoperable.

I know for a fact that our genetics are getting worse.

So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

Do common descent advocates get around this by hypothesizing a different world in the past, or do they simply ignore the facts?

let me ask Larry Gilman a question: Can you predict, with an overwhelming probability, what the religious affiliation will be of a boy born today in Islamabad?

I shouldn't wade into this, but how would you respond to the similar observation that the overwhelming majority of people accept what they were taught in science class. If 9th grade science books teach that there are three phases of mater, then people think there are three phases of mater. If four, then four. etc. To compound the problem, people who are serious about science and write those book assert that the majority of people are woefully scientifically ignorant. Similarly, the people who write books about religion, and teach religion classes assert that average people are woefully theologically ignorant.

Philip Bruce Heywood said: Torbjorn: you are a man of precision.

Philip Bruce Heywood said: I have heard - and I have every reason to believe it to be true - that the genetic damage constantly downgrading the clarity of genetically transmissible information in all higher life forms including Man, if it continues, will ultimately render higher life inoperable. I know for a fact that our genetics are getting worse.

So, evolution through mutation cannot happen amongst higher life-forms, IN THE ENVIRONMENT IN WHICH WE CURRENTLY LIVE.

prof weird said: That's a variant of the common creotard Information 'Argument' against evolution. Selection maintains the 'clarity' of genetic 'information' - variants of the 'information' that are not viable tend to go extinct very quickly.

Nigel D said:

Bobby said: Perhaps it's fraud, or perhaps it's merely the fact that IDologists, not being scientists in spirit, do not have any motivation to dig deeper when they see something that appears to support their agenda.

Bobby, this is very revealing. After the ID advocates have been whining on and on and on about how ID is science and not based on religion (oh, no, siree), even their own supporters are now admitting that they are not scientists. Whether this was a deliberate fraud or the result of academic incompetence is only a small difference. It illustrates the inherent hypocrisy of the entire ID movement. They are happy to accuse science of irrelevant wrongdoing (e.g. over Haeckel's embryo images, that were revealed to be wrong by scientists working about 100 years ago and are only included in textbooks to provide some historical perspective; and over the peppered moth images, which nicely illustrate the moths' camouflage irrespective of whether they are photographed on a tree trunk or a branch), but are not prepared even to attempt to meet the standard they publicly expect others to meet.

Bobby, you should report that to the admins. They do not tolerate sock-puppetry and other forms of deceptive posting. The offending poster can be ID-ed by their IP address and admonished (or banned).

Bobby said: Someone else used my name.

Richard Simons said:

Bobby said: Someone else used my name.

I had wondered if two people were posting under the name 'Bobby' on different threads as one seemed to accept evolution, the other not.

There are in this thread several comments whose two different authors used the same handle "Bobby." Their email addresses and IP's differ. Since "Bobby" is a rather common name, it is possible the two commenters happened to choose the same handle by accident, so I see no sufficient reasons to punish any of them. Indeed, the texts of their comments do not look like any of them aimed at undermining the position of the other "Bobby." Perhaps any of them (or both) would slightly modify their ID-handles to make clear who writes what?

"Bobby" - uppercase, the reasonable guy

"bobby" - lower case, juvenile idiot

I suggest the former change his moniker to something less common, and the latter's comments be deleted until he learns what it is to have adult conversation.

Ditto for Keith, Gary, and anyone else who routinely makes shit up, uses completely unecessary invectives, and ignores the questions posed and the answers offerred them. If you don't clear out the trolls, you are going to find this site populated with little else, which would be a damned shame. I for one used to learn a lot of biology here, back when the lowest-browed commentors weren't allowed to derail every thread into Loonyland.

Flint said: “Huh? First, as many many many demonstrations have shown, selection speeds up the appearance of functional structures by many orders of magnitude. It’s not pure accident; selection is very powerful.” Regarding bigbang’s “infinite number of organisms and time.”

.

Sure, selection, survival of the fittest, is indeed a truism. How could it be otherwise? And of course we know the traits that survive are the fittest b/c if they weren’t, they’d not have survived. Circular perhaps, but undeniably a truism.

The problem of course is what can random mutations actually provide for natural selection to select from?

As malaria expert N J White has determined, from actual data in the real world rather than just so stories, it took random mutation and selection working in a population of around 10^20 Malaria parasites/organisms to finally developed resistance to CQ, which required two mutations; two mutations (unlike resistance to most other drugs which generally require just one mutation, or perhaps more than one mutation attained by simple step by step selectable paths) that apparently were not attained by simple step by step selectable paths.

And since it’s estimated (by various experts) that there’ve been less than 10^40 cells in Earth’s 4 billion year history, and that most proteins in the cell operate as specific complexes of six or more chains, requiring five or more protein sites, and that developing new protein sites seems to require at least two or more mutations that can’t necessarily be obtained by simple step by step selectable paths, well, 10^40 organism just isn’t enough opportunity for random mutation and selection to work their magic and evolve things like flagella and sentient beings.

Ergo, we stipulate infinite organisms and time, making such things like flagella and sentient beings possible, and indeed inevitable. That’s the beauty of infinities----it’s similar to the infinite multiverse where all universes, including the one we now find ourselves in, are not only possible, but inevitable.

bigbang said: Flint said: “Huh? First, as many many many demonstrations have shown, selection speeds up the appearance of functional structures by many orders of magnitude. It’s not pure accident; selection is very powerful.” Regarding bigbang’s “infinite number of organisms and time.” . Sure, selection, survival of the fittest, is indeed a truism. How could it be otherwise? And of course we know the traits that survive are the fittest b/c if they weren’t, they’d not have survived. Circular perhaps, but undeniably a truism. The problem of course is what can random mutations actually provide for natural selection to select from? As malaria expert N J White has determined, from actual data in the real world rather than just so stories, it took random mutation and selection working in a population of around 10^20 Malaria parasites/organisms to finally developed resistance to CQ, which required two mutations; two mutations (unlike resistance to most other drugs which generally require just one mutation, or perhaps more than one mutation attained by simple step by step selectable paths) that apparently were not attained by simple step by step selectable paths. And since it’s estimated (by various experts) that there’ve been less than 10^40 cells in Earth’s 4 billion year history, and that most proteins in the cell operate as specific complexes of six or more chains, requiring five or more protein sites, and that developing new protein sites seems to require at least two or more mutations that can’t necessarily be obtained by simple step by step selectable paths, well, 10^40 organism just isn’t enough opportunity for random mutation and selection to work their magic and evolve things like flagella and sentient beings. Ergo, we stipulate infinite organisms and time, making such things like flagella and sentient beings possible, and indeed inevitable. That’s the beauty of infinities----it’s similar to the infinite multiverse where all universes, including the one we now find ourselves in, are not only possible, but inevitable.

I am not in the creationist camp at all, being an atheist, but I do have some skepticism concerning natural selection as the dominant mode of evolution. So I guess I should have at it with a couple of questions:

1.) According to Darwin, et al evolution is completely non-teleological (not end goal driven). Once a sufficiently advanced form of life (such as Homo sapiens) evolves doesn't the process now become teleological? We can decide which traits we want to develop in our own species as well as other species (not to mention which other species go extinct). So isn't evolution as it's operating now a teleological process? And if so how does it change the basic theory?

2.) The environment is the agent of selection or SELECTOR (if you will). I've always thought that this was too vaguely defined in evolutionary theory. What is the environment? The atmospheric composition of the planet? Yes. The gravitational field of the planet and its strength (e.g., 9.8 meters per second per second)? Yes. The particular landforms (e.g., rivers, canyons, marshes, oceans, etc., etc.)? Yes. The other organisms on the planet? Yes. But wait! Evolution is non-teleological. If you include other organisms (e.g., predators, prey, competitors) then this sets up feedback loops which make the system teleological. Example, a lion-like organism changes its hunting strategy which in turn causes the zebra-like organism to change its grazing behavior which in turn affects the predator, in a complex feedback loop. Environment and organism are now intertwined. WHAT/WHO is the SELECTOR as opposed to the SELECTEE now? It may be the organism itself which evolves itself - which breaks non-teleology.

3.) The environment has some sort of stability. It seems to me that a chaotically changing environment on a short time scale cannot drive evolution. Traits that are advantageous in one generation are disadvantageous in the next generation and therefore no secular evolution can happen. Doesn't the claim that natural selection has happened on Earth imply certain characteristics concerning the Earth's environment? There must be some stability to the environment in a time scale approaching the longevity of the organism itself. Has this type of stability really predominated the geophysical history of the earth? Maybe not, volcanoes erupt randomly, asteroids impact randomly, and according to the data in the Greenland ice sheet the average temperature in certain locations fluctuated by as much as 50 deg F per year which is huge.

4.) If we think of natural selection as movement of a population of points in some fitness landscape (consider a 2D grid with X being width and Y being length and a surface in a 3rd dimension defined by vertical Z being the fitness coefficient) then evolution can be thought of as the movement of a population of points in this fitness landscape. Question: In this scenario can natural selection produce results that are any better than the hill climbing algorithm (i.e., sample your immediate neighborhood and find the local slope of the landscape, then take a small step uphill)? If so then it is well known that the hill climbing algorithm can only find a local maximum and not the overall peak for the fitness landscape. Is there any evidence that natural selection can do better than this?

And thanks in advance for your answers to any of these questions.

Science Avenger said: If you don't clear out the trolls, you are going to find this site populated with little else, which would be a damned shame. I for one used to learn a lot of biology here, back when the lowest-browed commentors weren't allowed to derail every thread into Loonyland.

bigdumbliar: As malaria expert N J White has determined, from actual data in the real world rather than just so stories, it took random mutation and selection working in a population of around 10^20 Malaria parasites/organisms to finally developed resistance to CQ, which required two mutations; two mutations (unlike resistance to most other drugs which generally require just one mutation, or perhaps more than one mutation attained by simple step by step selectable paths) that apparently were not attained by simple step by step selectable paths.

1: Acta Trop. 2003 Mar;85(3):363-73. Links prevalence of quintuple mutant dhps/dhfr genes in Plasmodium falciparum infections seven years after introduction of sulfadoxine and pyrimethamine as first line treatment in Malawi.Bwijo B, Kaneko A, Takechi M, Zungu IL, Moriyama Y, Lum JK, Tsukahara T, Mita T, Takahashi N, Bergqvist Y, Björkman A, Kobayakawa T. Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-Cho, Shinjuku-Ku, Tokyo 162 8666, Japan. Malawi changed its national policy for malaria treatment in 1993, becoming the first country in Africa to replace chloroquine by sulfadoxine and pyrimethamine combination (SP) as the first-line drug for uncomplicated malaria. Seven years after this change, we investigated the prevalence of dihydropteroate synthase (dhps) and dihydrofolate reductase (dhfr) mutations, known to be associated with decreased sensitivity to SP, in 173 asymptomatic Plasmodium falciparum infections from Salima, Malawi. A high prevalence rate (78%) of parasites with triple Asn-108/Ile-51/Arg-59 dhfr and double Gly-437/Glu-540 dhps mutations was found. This 'quintuple mutant' is considered as a molecular marker for clinical failure of SP treatment of P. falciparum malaria. A total of 11 different dhfr and dhps combinations were detected, 3 of which were not previously reported. Nineteen isolates contained the single Glu-540 mutant dhps, while no isolate contained the single Gly-437 mutant dhps, an unexpected finding since Gly-437 are mostly assumed to be one of the first mutations commonly selected under sulfadoxine pressure. Two isolates contained the dhps single or double mutant coupled with dhfr wild-type. The high prevalence rates of the three dhfr mutations in our study were consistent with a previous survey in 1995 in Karonga, Malawi, whereas the prevalences of dhps mutations had increased, most probably as a result of the wide use of SP. A total of 52 P. falciparum isolates were also investigated for pyrimethamine and sulfadoxine/pyrimethamine activity against parasite growth according to WHO in vitro standard protocol. A pyrimethamine resistant profile was found. When pyrimethamine was combined with sulfadoxine, the mean EC(50) value decreased to less than one tenth of the pyrimethamine alone level. This synergistic activity may be explained by sulfadoxine inhibition of dhps despite the double mutations in the dhps genes, which would interact with pyrimethamine acting to block the remaining folate despite dhfr mutations in the low p-aminobenzoic acid and low folic acid medium mixed with blood.

I'll add here that focusing on mutations is so 2006. What is rate limiting in evolution seems to be the natural selection component of RM + NS.

We now know from sequencing multiple individual human genomes that somewhere between 100 and 175 new base differences appear from one generation to the next. The variability between 2 people is large, up to 15-20 million base pairs.

There is plenty of variability and it is being generated and shuffled constantly, every generation. We've seen selective sweeps of new alleles in almost real time, amylase copy number mutants and adult lactose tolerance. This fits in with punctuated equilibrium where periods of residence of a species at a local optimum is followed by rapid evolutionary change when the ecosphere optimum shifts.

Tom Marking said: 1.) According to Darwin, et al evolution is completely non-teleological (not end goal driven). Once a sufficiently advanced form of life (such as Homo sapiens) evolves doesn't the process now become teleological? We can decide which traits we want to develop in our own species as well as other species (not to mention which other species go extinct). So isn't evolution as it's operating now a teleological process? And if so how does it change the basic theory?

2.) The environment is the agent of selection or SELECTOR (if you will).

3.) The environment has some sort of stability.

Is there any evidence that natural selection can do better than this?

Partial reply to Tom Marking:
Dear Tom: Your comment contains a number of questions (of which many have been responded to more than once before). i'll not try to answer all your questions here but will instead only try to clarify for you just one point - that about evolutionary algorithms. The main fault of your discourse is that you consider a fitness landscape which is just two-dimensional (the third dimension being the fitness function itself). The real fitness landscapes in the biosphere are multi-dimensional. They usually have very few real peaks but instead many saddles, which appear like peaks in some of the dimensions, while hugging the rising slopes in many other directions, hence providing the hill-climbing algorithms plenty of ways to proceed beyond what may seem to be a local peak. Moreover, the real evolutionary algorithms are not necessarily hill-climbing. They are capable of not being stuck on a local maximum, even if such is encountered, but can very well descend into the neighboring depression in the fitness landscape, from which another upward slope may be emerging. In other words, the evolution not always is a continuous upward process, as an organism's fitness may as well decrease because of a certain mutation(s) but at a later stage pick up the upward ascent (fitness increase) again, in a different direction. You've imagined a substantially simplified model of evolution thus getting puzzled by non-existing obstacles to evolution which is in fact a a complex multidimensional process. As to the rest of your questions, like your seeming confusion regarding what is environment, there are many commenters to this thread who can elaborate on that point, which I leave to them (if they wish to do so). Just a few general statements. The evolutionary biology does not view natural selection as the sole evolution's driving force; there are various mechanisms, considered in the modern ET, besides natural selection, and the relative role of each of those mechanisms is being heatedly debated in the scientific literature day in and day out. If you wish to learn about it in a serious way, the only option is to study the up-to-date scientific literature, as popular publications can't provide an adequate clarification for your concerns.

Science Avenger said: "Bobby" - uppercase, the reasonable guy "bobby" - lower case, juvenile idiot I suggest the former change his moniker to something less common, and the latter's comments be deleted until he learns what it is to have adult conversation. Ditto for Keith, Gary, and anyone else who routinely makes shit up, uses completely unecessary invectives, and ignores the questions posed and the answers offerred them. If you don't clear out the trolls, you are going to find this site populated with little else, which would be a damned shame. I for one used to learn a lot of biology here, back when the lowest-browed commentors weren't allowed to derail every thread into Loonyland.

Tom Marking said: I am not in the creationist camp at all, being an atheist, but I do have some skepticism concerning natural selection as the dominant mode of evolution. So I guess I should have at it with a couple of questions: 1.) According to Darwin, et al evolution is completely non-teleological (not end goal driven). Once a sufficiently advanced form of life (such as Homo sapiens) evolves doesn't the process now become teleological? We can decide which traits we want to develop in our own species as well as other species (not to mention which other species go extinct). So isn't evolution as it's operating now a teleological process? And if so how does it change the basic theory?

2.) The environment is the agent of selection or SELECTOR (if you will). I've always thought that this was too vaguely defined in evolutionary theory. What is the environment? The atmospheric composition of the planet? Yes. The gravitational field of the planet and its strength (e.g., 9.8 meters per second per second)? Yes. The particular landforms (e.g., rivers, canyons, marshes, oceans, etc., etc.)? Yes. The other organisms on the planet? Yes. But wait! Evolution is non-teleological. If you include other organisms (e.g., predators, prey, competitors) then this sets up feedback loops which make the system teleological. Example, a lion-like organism changes its hunting strategy which in turn causes the zebra-like organism to change its grazing behavior which in turn affects the predator, in a complex feedback loop. Environment and organism are now intertwined. WHAT/WHO is the SELECTOR as opposed to the SELECTEE now? It may be the organism itself which evolves itself - which breaks non-teleology.

3.) The environment has some sort of stability. It seems to me that a chaotically changing environment on a short time scale cannot drive evolution. Traits that are advantageous in one generation are disadvantageous in the next generation and therefore no secular evolution can happen. Doesn't the claim that natural selection has happened on Earth imply certain characteristics concerning the Earth's environment? There must be some stability to the environment in a time scale approaching the longevity of the organism itself. Has this type of stability really predominated the geophysical history of the earth? Maybe not, volcanoes erupt randomly, asteroids impact randomly, and according to the data in the Greenland ice sheet the average temperature in certain locations fluctuated by as much as 50 deg F per year which is huge.

4.) If we think of natural selection as movement of a population of points in some fitness landscape (consider a 2D grid with X being width and Y being length and a surface in a 3rd dimension defined by vertical Z being the fitness coefficient) then evolution can be thought of as the movement of a population of points in this fitness landscape. Question: In this scenario can natural selection produce results that are any better than the hill climbing algorithm (i.e., sample your immediate neighborhood and find the local slope of the landscape, then take a small step uphill)? If so then it is well known that the hill climbing algorithm can only find a local maximum and not the overall peak for the fitness landscape. Is there any evidence that natural selection can do better than this?

And thanks in advance for your answers to any of these questions.

The real fitness landscapes in the biosphere are multi-dimensional. They usually have very few real peaks but instead many saddles, which appear like peaks in some of the dimensions, while hugging the rising slopes in many other directions, hence providing the hill-climbing algorithms plenty of ways to proceed beyond what may seem to be a local peak.

raven said: On evolutionary relevant timescales, nothing is going to be the same for long. If it wasn't for Chickxulub, we probably wouldn't be here.

Tom Marking,

Re "So isn’t evolution as it’s operating now a teleological process?"

I suppose the parts that are under human influence might be. The parts that aren't, not. Developing traits in ourselves seems unlikely, since it would leave the question of who decides who gets to mate with who.

Re "What is the environment?"

Anything and everything (besides itself) that affects the reproductive success of the species. (This includes other species that are also evolving at the same time.)

Re "then this sets up feedback loops which make the system teleological."

Feedback loops can cause a trait to become more pronounced over time (for example, legs getting longer, or body size getting bigger, or in some cases smaller). But that's not what I thought "teleological" meant.

Re "It seems to me that a chaotically changing environment on a short time scale cannot drive evolution."

That makes sense to me, but the planet has plenty of environments that stay more or less stable for long periods; otherwise our civilization would be in trouble.

Henry

Many thanks to those who answered Mr. Markings questions, and of course him for raising them in the first place. The answers have been very informative.

Tom Marking said: 4.) If we think of natural selection as movement of a population of points in some fitness landscape (consider a 2D grid with X being width and Y being length and a surface in a 3rd dimension defined by vertical Z being the fitness coefficient) then evolution can be thought of as the movement of a population of points in this fitness landscape. Question: In this scenario can natural selection produce results that are any better than the hill climbing algorithm (i.e., sample your immediate neighborhood and find the local slope of the landscape, then take a small step uphill)? If so then it is well known that the hill climbing algorithm can only find a local maximum and not the overall peak for the fitness landscape. Is there any evidence that natural selection can do better than this?

Mike Elzinga said: If the Bathroom Wall is not adequate, why not institute a Psychiatric Ward or Padded Cell for these trolls?

Raven says: “The only 2 mutations possible nonsense was a lie when Behe said it. If he had spent 5 minutes checking the malaria drug resistance literature, he would have found triple, quadruple, and quintuple mutants killing people right and left.”

.

A lie? My, my, raven, you people do get malicious, don’t you?

And as it turns out, Behe did check out and discuss sulfadoxine/pyrimethamine, or S/P (in his EoE), being used in Malawi starting in 1993, after CQ was discontinued; and that resistance to the “P” developed via mutation in the DHFR enzyme (changing the amino acid at position 108 from serine to asparagines), and also developed a resistance to “S” via mutation to the DHPS enzyme (changing the alanine to glycine at position 437). (Behe also notes that that about five years after the S/P was used in Malawi, the malaria there became susceptible to CQ again.)

Still raven, you’re missing the point----the CQ resistance required two mutations, that obviously couldn’t be attained by simple step by step selectable paths; and as determined by N J White, no matter how you cut it, the data shows us that random mutation and selection had to go through 10^20 organisms b/f attaining the required mutations. Got that?----It’s actual data that gives us the 10^20, regardless of whatever you happen to believe regarding the required mutations. Unlike resistance to various other drugs which requires just one mutation where random mutation and selection have to go through maybe only 10^12 organisms.

And, as I’ve noted, since it’s estimated (by various experts) that there’ve been less than 10^40 cells in Earth’s 4 billion year history, and that most proteins in the cell operate as specific complexes of six or more chains, requiring five or more protein sites, and that developing new protein sites seems to require at least two or more mutations that can’t necessarily be obtained by simple step by step selectable paths, then 10^40 organism just isn’t enough opportunity for random mutation and selection to work their magic and evolve things like flagella and sentient beings. Ergo the need for infinities.

Still raven, you’re missing the point—-the CQ resistance required two mutations, that obviously couldn’t be attained by simple step by step selectable paths; and as determined by N J White, no matter how you cut it, the data shows us that random mutation and selection had to go through 10^20 organisms b/f attaining the required mutations. Got that?—

The estimates for chloroquine and artemisinin are speculative. In the former case, this assumes two events in 10 years of use with exposure of 10% of the world’s falciparum malaria (Burgess &Young 1959; Martin&Arnold1968; Looareesuwan et al. 1996; Su et al. 1997

phantomreader42 said: Garbage. Regurgitating crap that's already been debunked on this very site. Can't you morons even come up with any NEW lies?

Bigdumblier again: A lie? My, my, raven, you people do get malicious, don’t you?

2006 | Volume : 52 | Issue : 4 | Page : 271-276 Current understanding of the molecular basis of chloroquine-resistance in Plasmodium falciparum Jiang H, Joy DA, Furuya T, Su X-z Despite multiple independent origins of CQR worldwide, CQR parasites share some common phenotypes: (1) increased IC 50 , deleted for length Twenty point mutations have been found in the pfcrt gene to date from CQR field isolates or laboratory clones through drug selection.[5] Association studies have shown that substitution of threonine (T) for lysine (K) at position 76 (K76T) is the hallmark of CQR parasites worldwide.[23],[25],[26] Although a few exceptions (e.g ., parasites with 76T allele of pfcrt were cleared by CQ treatment or parasites survived the CQ treatment while carrying 76K allele) have been reported recently,

Bigdumbliar: Still raven, you’re missing the point—-the CQ resistance required two mutations, that obviously couldn’t be attained by simple step by step selectable paths;

raven said: Behe's pseudoscience was trashed immediately by the scientific community as incredibly poor scholarship.

J Infect Dis. 2006 May 1;193(9):1304-12. Epub 2006 Mar 21. Links Progressive increase in point mutations associated with chloroquine resistance in Plasmodium falciparum isolates from India.Mittra P, Vinayak S, Chandawat H, Das MK, Singh N, Biswas S, Dev V, Kumar A, Ansari MA, Sharma YD. Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India. BACKGROUND: Effective malaria control programs require continuous monitoring of drug pressure in the field, using molecular markers. METHODS: We used sequence analysis to investigate the pfcrt and pfmdr1 mutations in Indian Plasmodium falciparum isolates. To evaluate the chloroquine drug pressure in the field, isolates were collected from 5 different areas at 2 time points, with an interval of 2 years. RESULTS: In 265 P. falciparum isolates, pfcrt mutations were observed at codons 72, 74, 75, 76, and 220, resulting in 8 different genotypes: SMNTS (61.89%), CIETS (12.08%), CMNKS (0.38%), CMNTA (2.64%), CMNTS (4.91%), SMNTA (0.38%), CIDTS (2.26%), and wild-type CMNKA (15.47%). During the 2-year period, there was a significant decrease in the number of isolates with the SMNTS genotype and an increase in the number of isolates with the highly chloroquine-resistant pfcrt genotype CIETS (P less than .05). The N86Y mutation was less prevalent (30.13%) than the Y184F mutation (99.16%) in the pfmdr1 gene in 239 isolates, but the number of isolates with the N86Y mutation increased significantly during the 2-year period (P less than .05). The number of isolates with higher total numbers of pfcrt and pfmdr1 2-loci mutations, therefore, increased significantly during this period. There was a regional bias in the mutation rate of these genes, because isolates from areas where chloroquine resistance was high had higher numbers of 2-loci mutations, and areas where chloroquine resistance was low had isolates with lower numbers of 2-loci mutations. CONCLUSION: There was a temporal increase in the number of pfcrt and pfmdr1 2-loci mutations, and this led to the higher level of chloroquine resistance. This is a cause for concern for the antimalarial drug policy in India.

Neo-Anti-Luddite, Prof.Weird, Torbjorn,O.M..

What I am not, is a genetics expert/engineer. Listening to news reports, reading the science stuff - I have gained the clear impression that it is a fact that human health defects traceable to inheritance are increasing, and theoretically will do so unless something can be done to stop it. I think I am 100% correct on that. Am I?

But the reverse is true, in the case of harmful micro-organisms. They just keep improving. Correct or no?

Philip Bruce Heywood said: Neo-Anti-Luddite, Prof.Weird, Torbjorn,O.M.. What I am not, is a genetics expert/engineer. Listening to news reports, reading the science stuff - I have gained the clear impression that it is a fact that human health defects traceable to inheritance are increasing, and theoretically will do so unless something can be done to stop it. I think I am 100% correct on that. Am I? But the reverse is true, in the case of harmful micro-organisms. They just keep improving. Correct or no?

Philip Bruce Heywood said: ...What I am not, is a genetics expert/engineer.

Listening to news reports, reading the science stuff - I have gained the clear impression that it is a fact that human health defects traceable to inheritance are increasing, and theoretically will do so unless something can be done to stop it. I think I am 100% correct on that. Am I?

But the reverse is true, in the case of harmful micro-organisms. They just keep improving. Correct or no?

Mol Pharmacol. 2002 Jan;61(1):35-42. Links Alternative mutations at position 76 of the vacuolar transmembrane protein PfCRT are associated with chloroquine resistance and unique stereospecific quinine and quinidine responses in Plasmodium falciparum.Cooper RA, Ferdig MT, Su XZ, Ursos LM, Mu J, Nomura T, Fujioka H, Fidock DA, Roepe PD, Wellems TE. National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. Chloroquine resistance (CQR) in Plasmodium falciparum is associated with multiple mutations in the digestive vacuole membrane protein PfCRT. The chloroquine-sensitive (CQS) 106/1 line of P. falciparum has six of seven PfCRT mutations consistently found in CQR parasites from Asia and Africa. The missing mutation at position 76 (K76T in reported population surveys) may therefore be critical to CQR. To test this hypothesis, we exposed 106/1 populations (10(9)-10(10) parasites) to a chloroquine (CQ) concentration lethal to CQS parasites. In multiple independent experiments, surviving CQR parasites were detected in the cultures after 28 to 42 days. These parasites showed novel K76N or K76I PfCRT mutations and corresponding CQ IC(50) values that were approximately 8- and 12-fold higher than that of the original 106/1 IC(50). A distinctive feature of the K76I line relative to 106/1 parasites was their greatly increased sensitivity to quinine (QN) but reduced sensitivity to its enantiomer quinidine (QD), indicative of a unique stereospecific response not observed in other CQR lines. Furthermore, verapamil had the remarkable effect of antagonizing the QN response while potentiating the QD response of K76I parasites. In our single-step drug selection protocol, the probability of the simultaneous selection of two specific mutations required for CQR is extremely small. We conclude that the K76N or K76I change added to the other pre-existing mutations in the 106/1 PfCRT protein was responsible for CQR. The various mutations that have now been documented at PfCRT position 76 (K76T, K76N, K76I) suggest that the loss of lysine is central to the CQR mechanism.

Stanton said:

raven said: Behe's pseudoscience was trashed immediately by the scientific community as incredibly poor scholarship.

Why is it that these moronic Intelligent Design groupies can never understand that it's a matter of quality control?

Something looks designed. So what? Snowflakes look designed; that cloud from your childhood that looked like a unicorn looks designed.

A successful test of actual design could focus on the anticipatory moves of a real agent. Even a chipped flake could meet that test.

The ID crowd won't specify the nature of agency because they want to infer it tautologically while plugging in magic premises. Doesn't the appeal to design hurt their case when you come right down to the nuts and bolts of how agents really do design stuff?

What agents. Secret agents? Not agen(t)cies of design! Kick him down the stairs.

Nige, I know the human genome isn't changing. Torbjorn says it is - he says we are evolving, right now. Your reply was an improvement on Strife'sGrandmother's.

I was asking the three wise men whether they know if the genetic damage we are sustaining is indeed as I have been informed - increasing. I shall compare your thoughts with theirs.

Raven says: “Behe didn’t even get the two mutation data right. The main mutation to chlorquine resistance is a mutation called K76T. This can be found with up to 19 other known different mutations. A lot of in vivo and in vitro data indicate that K76T is the main mutation and the others most likely just potentiate it.”

.

Raven, I find your intellectual honesty and rigor less than compelling. You, like so many on your side of the argument, obviously haven’t actually and/or honestly considered, or simply don’t grasp, the data and arguments that Behe provides.

Behe discusses CQ resistance at some length in his EoE, noting that the mutant PfCRTs (the sequence of protein that provides the resistance) exhibits a range of changes, affecting as few as four amino acids to as many as eight; but the same two amino acid changes are almost always present----one switch at position 76 and another at position 220; and that the other mutations in the protein differ from each other with one group of mutations common to CQ resistant parasites in South America, and a second clustering of mutations appearing in malaria from Asia and Africa.

I must say raven that in all the back-and-forths that I’ve seen and studied between Behe and various neo-Darwinians (e.g. Behe’s blog at Amazon), a fair reading of those debates always shows that Behe exhibits far more intellectual honesty and rigor than his neo-Darwinian critics. And let’s be real raven----most who have some appreciation for the complexity and, dare I say, elegance, of life, especially at the molecular level, would agree that evolution by random mutation and selection is an incomplete theory at best (unlike, say, common descent for which there is indeed a good amount of evidence).

.

PvM says: “Behe is trying to credit White for his 10^20 however, White at least admits it’s a guestimate at best. Why would Behe use data which are so poorly supported?"

.

It’s a reasonably well supported and conservative estimate based on available and actual data, used in an attempt to reasonably and conservatively quantify what random mutation and selection has and can actually accomplish; unlike the typical unquantified just so stories that neo-Darwinians typically employ to explain the miracles of random mutation and selection that evolved all the amazing things we see today, such as flagella and sentient beings.

One last thing: Rather than blindly criticizing Behe for what so many of you blindly assume about him, you should take the time to actually read and study his EoE, and also to carefully read and consider the various back-and-forths with his critics in his Amazon blog----even though most of you will never agree with his conclusion regarding ID, Behe is a bright guy and the book is very well written with many, many solid sources documenting (and quantifying) his conclusions regarding the shortcomings of evolution via random mutation and selection (and remember that Behe has always acknowledged that the evidence for common descent is abundant, so common descent, contrary to what some of his disingenuous critics have alleged, has never been an issue).

Raven says: "I hate to beat a dead horse or a braindead creo (Behe and the troll)…."

.

Apparently raven rather enjoys beating his dead horse; and his puerile comments reveal much about him. Unfortunately, such behavior and commentary seems to be common among the true believers of random mutation and selection. Oh well.

Bigdumbliar: Apparently raven rather enjoys beating his dead horse; and his puerile comments reveal much about him. Unfortunately, such behavior and commentary seems to be common among the true believers of random mutation and selection. Oh well.

Bigdumbliar Making Things Up: And let’s be real raven—-most who have some appreciation for the complexity and, dare I say, elegance, of life, especially at the molecular level, would agree that evolution by random mutation and selection is an incomplete theory at best (unlike, say, common descent for which there is indeed a good amount of evidence).

And let’s be real raven—-most who have some appreciation for the complexity and, dare I say, elegance, of life, especially at the molecular level, would agree that evolution by random mutation and selection is an incomplete theory at best (unlike, say, common descent for which there is indeed a good amount of evidence)

And let’s be real raven—-most who have some appreciation for the complexity and, dare I say, elegance, of life, especially at the molecular level, would agree that evolution by random mutation and selection is an incomplete theory at best (unlike, say, common descent for which there is indeed a good amount of evidence)

Philip Bruce Heywood said: I was asking the three wise men whether they know if the genetic damage we are sustaining is indeed as I have been informed - increasing.

This means that we see an exponential decay of the current wild type phenotype with a half-life of roughly 7,000 years.

A lie? My, my, raven, you people do get malicious, don’t you?

— bigbang the troll

Is there a way to embed equations in here? I might be more apt to show calculations if it weren't so darn ugly to do so.

Larry Boy said: Is there a way to embed equations in here? I might be more apt to show calculations if it weren't so darn ugly to do so.

Philip Bruce Heywood said: ...Nige, I know the human genome isn't changing. Torbjorn says it is - he says we are evolving, right now. Your reply was an improvement on Strife'sGrandmother's. I was asking the three wise men whether they know if the genetic damage we are sustaining is indeed as I have been informed - increasing. I shall compare your thoughts with theirs.

Behe discusses CQ resistance at some length in his EoE, noting that the mutant PfCRTs (the sequence of protein that provides the resistance) exhibits a range of changes, affecting as few as four amino acids to as many as eight; but the same two amino acid changes are almost always present—-one switch at position 76 and another at position 220; and that the other mutations in the protein differ from each other with one group of mutations common to CQ resistant parasites in South America, and a second clustering of mutations appearing in malaria from Asia and Africa.

— bigbang

Raven says to bigbang: “You lie,” and that “Acceptance of evolution among scientists….”

.

No, I’m not the one being dishonest here.

Most everyone accepts, except perhaps raven’s straw man “creo,” which obviously neither Behe nor or I are, that life evolves, or unfolds as it were; and also in the reality of common descent. Furthermore, most would more or less accept so-called natural selection, or survival of the fittest, since it’s essentially a truism, albeit circular and doesn’t truly explain or predict much of anything except the circular and obvious, that the fittest traits survive in whatever environment those traits are determined to be the fittest. For example, CQ resistant malaria survives and outbreeds other strains of malaria in an environment where CQ is being used, but then peters out when CQ is no longer being used; as was the case in Malawi about five years after S/P had been used to fight Malaria.

What raven is unable to grasp is that the only actual issue is how much evolution can reasonably, quantifiably, be attributed to random mutation and selection pressures. Not all that much.

As the eminent geneticist Francois Jacob noted, Darwinian evolution, via random mutation and selection, is a tinkerer, not an engineer. Hell raven, even PvM, above, seems to acknowledge that random mutation and selection is an incomplete theory.

Nigel D says: “The mutation of K76 alone is sufficient to confer a significant degree of chloroquine resistance. This is, as Raven points out, potentiated by other, auxiliary mutations.”

.

Hmmm, imagine that, only one mutation, potentiated by other mutations (and/or perhaps by simple step by step selectable paths?), and yet it still took random mutation and selection 10^20 organisms, as determined from the available data by N J White, b/f malaria acquired the effective CQ resistance we’re talking about here . . . which, if you think about it, only strengthens the case against random mutation and selection. Thanks Nigel.

bigbang said: Raven says to bigbang: “You lie,” and that “Acceptance of evolution among scientists….” . No, I’m not the one being dishonest here. Most everyone accepts, except perhaps raven’s straw man “creo,” which obviously neither Behe nor or I are, that life evolves, or unfolds as it were; and also in the reality of common descent. Furthermore, most would more or less accept so-called natural selection, or survival of the fittest, since it’s essentially a truism, albeit circular and doesn’t truly explain or predict much of anything except the circular and obvious, that the fittest traits survive in whatever environment those traits are determined to be the fittest. For example, CQ resistant malaria survives and outbreeds other strains of malaria in an environment where CQ is being used, but then peters out when CQ is no longer being used; as was the case in Malawi about five years after S/P had been used to fight Malaria. What raven is unable to grasp is that the only actual issue is how much evolution can reasonably, quantifiably, be attributed to random mutation and selection pressures. Not all that much. As the eminent geneticist Francois Jacob noted, Darwinian evolution, via random mutation and selection, is a tinkerer, not an engineer. Hell raven, even PvM, above, seems to acknowledge that random mutation and selection is an incomplete theory. Nigel D says: “The mutation of K76 alone is sufficient to confer a significant degree of chloroquine resistance. This is, as Raven points out, potentiated by other, auxiliary mutations.” . Hmmm, imagine that, only one mutation, potentiated by other mutations (and/or perhaps by simple step by step selectable paths?), and yet it still took random mutation and selection 10^20 organisms, as determined from the available data by N J White, b/f malaria acquired the effective CQ resistance we’re talking about here . . . which, if you think about it, only strengthens the case against random mutation and selection. Thanks Nigel.

I’m a little late to the ball, but I’d like add my answers to Tom Marking’s questions. Keep in mind I’m a lowly chemist…

1)There are many types of selection. Natural selection, sexual selection, artificial selection (aka breeding), etc… The importance of each may vary with circumstances, but the use of artificial selection in humans, by humans does not mean natural selection stops or becomes teleological.

2) When Darwin wrote Origin he proposed that the selection pressure created by other species (e.g. cheetah – gazelle) was much stronger than the selection pressure created by the nonliving environment (e.g. temperature). I think modern biologists would say the answer is more nuanced, but at a minimum you are right in thinking natural selection means there will be a lot of feedback (and feedforward) loops. To be honest, I’m not sure how the existence of cheetahs makes gazelle evolution teleological, or why that’s even important. If natural selection fits someone’s definition of teleological, does the theory suddenly become wrong? Does it break a rule of science to say cheetahs and gazelles are in an arms race? I can’t see why it would.

3) It appears to me that the Earth has many environments that are stable over the lifetime of various organisms. Why, we haven’t had an ice age, volcanic eruption, or major meteor impact in my neighborhood for something like 1000 human lifetimes.

4) Yes, evolution is much more likely to find a local fitness maximum than a global one. Actually this is a classic argument against creation/intelligent design; if things were designed intelligently, we’d expect to see more body parts that are global fitness maxima (as far as we can tell). But instead we see things like the vascular nerve of the giraffe, and the ‘reverse’ orientation of photoreceptors in the mammalian eye – cases of obvious local maxima. Nor do creationist claims of degeneration successfuly explain these local maxima, because in fitness geometries like the simple one you describe it is as impossble to "jump down" to local maximum from a higher one as it is to "jump up" to a higher one from a lower one. Degeneration has no way of looping a vascular nerve around the aorta.

If you think about it, your simple local maxima analogy is just a biological reframing of the problem of evil. Frankly it has always surprised me that IDers wanted to put the problem of evil up for discussion in a classroom. That particular philosophical discussion is not known for creating religious converts.

bigbang said: Hmmm, imagine that, only one mutation, potentiated by other mutations (and/or perhaps by simple step by step selectable paths?), and yet it still took random mutation and selection 10^20 organisms, as determined from the available data by N J White, b/f malaria acquired the effective CQ resistance we’re talking about here … which, if you think about it, only strengthens the case against random mutation and selection. Thanks Nigel.

eric said: Does it break a rule of science to say cheetahs and gazelles are in an arms race? I can’t see why it would.

Larry boy writes... I shouldn’t wade into this, but how would you respond to the similar observation that the overwhelming majority of people accept what they were taught in science class. If 9th grade science books teach that there are three phases of mater, then people think there are three phases of mater. If four, then four. etc.

If we think of natural selection as movement of a population of points in some fitness landscape (consider a 2D grid with X being width and Y being length and a surface in a 3rd dimension defined by vertical Z being the fitness coefficient) then evolution can be thought of as the movement of a population of points in this fitness landscape. Question: In this scenario can natural selection produce results that are any better than the hill climbing algorithm (i.e., sample your immediate neighborhood and find the local slope of the landscape, then take a small step uphill)? If so then it is well known that the hill climbing algorithm can only find a local maximum and not the overall peak for the fitness landscape. Is there any evidence that natural selection can do better than this?

"The real fitness landscapes in the biosphere are multi-dimensional. They usually have very few real peaks but instead many saddles, which appear like peaks in some of the dimensions, while hugging the rising slopes in many other directions"

Yes, I realize that the real dimensionality of the problem is something like ~10,000 (or ~20,000 for humans if you want to equate the cardinality of the trait space with the total number of genes). I used the 3D version for simplicity. It is very hard to get one's mind around what a "saddle shape" is in 10,000 dimensions. I have a hard time visualizing that.

"Moreover, the real evolutionary algorithms are not necessarily hill-climbing. They are capable of not being stuck on a local maximum, even if such is encountered, but can very well descend into the neighboring depression in the fitness landscape, from which another upward slope may be emerging."

Hmmm, I'm finding that a hard concept to grasp. Wouldn't natural selection prohibit the movement of the center of gravity of the population towards lower fitness? Such mutations in that direction would be weeded out in the very first generation they occur in, right? Maybe if the distance to the next upward slope was not that far then some temporary lowering of fitness could happen which enables the population to jump to the other hill. I'm not sure if you had that in mind. It seems to go against the concept of incremental change.

And, as I’ve noted, since it’s estimated (by various experts) that there’ve been less than 10^40 cells in Earth’s 4 billion year history, and that most proteins in the cell operate as specific complexes of six or more chains, requiring five or more protein sites, and that developing new protein sites seems to require at least two or more mutations that can’t necessarily be obtained by simple step by step selectable paths, then 10^40 organism just isn’t enough opportunity for random mutation and selection to work their magic and evolve things like flagella and sentient beings. Ergo the need for infinities.

"Random Mutation is not goal driven. You cannot select something if it doesn’t exist. One could argue that breeding programs are artificial selection instead of NS, but it is still selection. You may get something that is the more perfect cow, horse or whatever, but you can’t just “design” a cow that has twice as much filet mignon."

The mutations themselves are not goal driven since, of course, they are random. That says nothing about the selection of such mutations being goal driven or not. Given the incredible results of artificial selection which human beings have carried out during the last 10,000 years I would say that a Black Angus is precisely a cow which has been "designed" to have twice as much filet mignon as the original wild type.

If he did, then perhaps white is wrong. Scientist make mistakes with math all the time. How did White make his estimate? Walk me through the math and measurements he took to get there.

The de novo selection of drug-resistant malaria parasites N. J. White1,2* and W. Pongtavornpinyo2 Proc Royal Society Biology 2003 Table 1. Approximate per-parasite frequencies for genetic events (mutations or gene amplifications) which lead to the emergence of clinically significant drug resistance of Plasmodium falciparum in vivo. (If the resistance mechanism is multigenic then this represents the frequency of the parasite becoming resistant and thus it is the product of the individual mutation frequencies. The estimate for pyrimethamine is for the drug alone. When it is combined together with a sulphonamide the frequency appears to be significantly lower. The estimate for mefloquine is in already chloroquine-resistant parasites. The estimates for chloroquine and artemisinin are speculative. In the former case, this assumes two events in 10 years of use with exposure of 10% of the world’s falciparum malaria (Burgess & Young 1959; Martin & Arnold 1968; Looareesuwan et al. 1996; Su et al. 1997; Nosten et al. 2000).) drug per-parasite resistance mutation frequency pyrimethamine 1 in 10exp11 atovaquone 1 in 10exp12 mefloquine 1 in 10exp14 chloroquine 1 in 10exp19 artemisinin ,1 in 10exp18

Hmmm, I’m finding that a hard concept to grasp. Wouldn’t natural selection prohibit the movement of the center of gravity of the population towards lower fitness? Such mutations in that direction would be weeded out in the very first generation they occur in, right? Maybe if the distance to the next upward slope was not that far then some temporary lowering of fitness could happen which enables the population to jump to the other hill. I’m not sure if you had that in mind. It seems to go against the concept of incremental change.

Hmmm, I’m finding that a hard concept to grasp. Wouldn’t natural selection prohibit the movement of the center of gravity of the population towards lower fitness?

"Re “What is the environment?”

Anything and everything (besides itself) that affects the reproductive success of the species. (This includes other species that are also evolving at the same time.)"

Let me explain why I think there is a philosophical problem with this. You might want to define the theory of natural selection as follows:

1.) The environment causes differential reproductive success in a population of organisms thus driving evolution.

But if your definition for environment is:

2.) The environment is the totality of physical factors which causes differential reproductive success in a population of organisms

Then you haven't really specified what it is exactly that is causing the reproductive success. It is essentially a tautology.

Now, you might claim that, for example, Newton's 2nd Law, is also tautological. Thus:

3.) Force equals mass times acceleration

4.) Force is that which given a value of F and applied to a mass of M causes an acceleration of F/M

Let me explain why in this case Newton's 2nd Law is not tautological. In a nutshell, the methodology for measuring F, M, and A are all different. F is measured with a spring, M is measured with a balance using standard weights, and A can be measured by looking at the motion of the object in question.

In the case of natural selection, the end result of differential reproductive success is measured (in most cases) by looking at changes in the fossil record. How is the environment measured?

If you were to tell me that environment was measured by looking at the ratio of O-18 to O-16 isotopes in sea floor sediment which can be used to deduce temperature, and other things like that then I have no problem with it. It's not a tautology. However, in the vast majority of cases all we have are the changes in the fossil record. It seems only in the cases of extreme environmental stress (e.g., KT impactor, Siberian Traps causing Permian extinction) do we have a separately measurable environmental factor directly linked to evolutionary change in the fossil record.

So in most cases of evolution we must assume that something in the environment was causing the evolution, but as to exactly what it was, we don't know and probably can never know.

And if we include species-to-species feedback effects with thousands of species and tens of thousands of genes per species, the actual "cause" of any evolutionary event may be more complicated than the human mind can understand anyway.

I should add that in high dimensional fitness landscapes it is exceedingly unlikely that a local maximum is extreme enough to prohibit peak-hopping.

bigbang said: And of course we know the traits that survive are the fittest b/c if they weren’t, they’d not have survived. Circular perhaps, but undeniably a truism.

Tom Marking said: 1.) According to Darwin, et al evolution is completely non-teleological (not end goal driven). Once a sufficiently advanced form of life (such as Homo sapiens) evolves doesn't the process now become teleological? We can decide which traits we want to develop in our own species as well as other species (not to mention which other species go extinct). So isn't evolution as it's operating now a teleological process? And if so how does it change the basic theory?

Tom Marking said: 2.) The environment is the agent of selection or SELECTOR (if you will). I've always thought that this was too vaguely defined in evolutionary theory. What is the environment?

Tom Marking said: If you include other organisms (e.g., predators, prey, competitors) then this sets up feedback loops which make the system teleological.

Tom Marking said: It seems to me that a chaotically changing environment on a short time scale cannot drive evolution. Traits that are advantageous in one generation are disadvantageous in the next generation and therefore no secular evolution can happen.

Tom Marking said: If so then it is well known that the hill climbing algorithm can only find a local maximum and not the overall peak for the fitness landscape. Is there any evidence that natural selection can do better than this?

Tom Marking said: So in most cases of evolution we must assume that something in the environment was causing the evolution, but as to exactly what it was, we don't know and probably can never know.

Sun Spiker says: “So really what you are saying is that Behe (or you) has discovered that evolution as we know it is wrong….”

.

Well, no Spiker, not exactly. Let me splain it again----what we observe is that although it’s fairly clear that life has and continues to evolve, and that there’s plenty of evidence for common descent, it’s just that evolution by random mutation and selection is obviously quite limited. Although random mutation and selection certainly seems to explain things like drug resistance by various organisms/viruses, and things like the single mutation that has resulted in a change in the hemoglobin protein site causing sickle cell in humans, which provides protection against malaria----but which is actually a degradation of hemoglobin making it less efficient and, unfortunately, also causes sickle cell disease in those individuals having two sickle cell genes, one from each parent----it just doesn’t really, in any meaningful and coherent way, truly explain most of the evolution of say flagellum, or the complexity of eukaryotic cells, or sentient beings.

So I suppose you could say that we’re simply taking note of the obvious, that evolution by random mutation and selection is really quite limited, an incomplete theory of sorts. But you neo-Darwinians really shouldn’t feel so bad about that since even Newton’s superb and elegant theory was found to be incomplete once Einstein discovered his general relativity . . . you know, the Einstein that saw a “spirit manifest in the laws of the Universe—a spirit vastly superior to that of man.”

Hell, even a hardcore neo-Darwinian Kenneth Miller believes in design, since, after all, he is a Catholic/theist of sorts; it’s just that he apparently believes that design only goes as far as, say, the laws of physics, and apparently doesn’t believe that design goes as deep as, say, the microbiologist Behe thinks it goes; so really it’s just a matter of degree, isn’t it? Except of course for the neo-Darwinian atheists that see no design whatsoever, but rather see only randomness and accidents, and, I suppose, what Dawkins what has hailed the non-random force of natural selection.

.

Larrson said: “And of course we know the bodies that move are the most energetic b/c if they weren’t, they’d not have moved. Circular perhaps, but undeniably a truism.”

.

You’re probably thinking of some sort of equation. Not that it matters but equations quantify the theories/natural laws that have been discovered by physicists which are then used to predict things; the terms on both sides of an equation are typically defined elsewhere; the equal sign does not mean "is defined by, " it means is equal to. Equations are not tautologies, are not circular. Fitness, on the other hand is defined by selection-----see the difference? Still, selection is not the issue; selection pressures seem to be undeniable; it just that selection is circular and that we can’t really predict anything terribly specific, except the obvious, that the fittest traits survive.

Raven says: “His guess is 1 in 10exp19, not 1 in 10exp20.”

.

Wrong paper, wrong number, raven. Refer to White, N. J. 2004; Antimalrial drug resistence; J Clin.Invest; 113:1084-92. Resistance to CQ has appeared fewer than ten times in the past half century. White notes that if you multiply the number of parasites in a person very ill with malaria, times the number of people who get malaria per year, times the number of years since the introduction of CQ, then you can estimate that the odds of a parasite developing resistance to CQ is roughly one in 10^20.

But what the hell raven, if your prefer the 10^19 number, and think the 10 fold difference will really matter all that much, plug it in and see what you get. Really raven, do yourself a favor and actually read and consider Behe’s EoE. Behe is a lot more meticulous than you and his many of critics give him credit for.

If Behe is so meticulous in his work, then how come he acts as though no one has ever done any work on studying the evolutionary histories of the vertebrate immune system, the vertebrate blood-clotting cascade system, or bacterial and eukaryotic flagella (not to mention archaean flagella) since he published "Darwin's Black Box," if he admits that anyone did any work on any of those topics to begin with?

Raven says: “The edge of evolution is known for now. Just look around. We are it. So is my cat.”

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No no raven, he actual issue is just the edge of evolution via random mutations and selection. Understand? Why can’t you people seem to remember that? Or are you just being disingenuous?

bigbang said: Raven says: “His guess is 1 in 10exp19, not 1 in 10exp20.” . Wrong paper, wrong number, raven. Refer to White, N. J. 2004; Antimalrial drug resistence; J Clin.Invest; 113:1084-92. Resistance to CQ has appeared fewer than ten times in the past half century. White notes that if you multiply the number of parasites in a person very ill with malaria, times the number of people who get malaria per year, times the number of years since the introduction of CQ, then you can estimate that the odds of a parasite developing resistance to CQ is roughly one in 10^20. But what the hell raven, if your prefer the 10^19 number, and think the 10 fold difference will really matter all that much, plug it in and see what you get. Really raven, do yourself a favor and actually read and consider Behe’s EoE. Behe is a lot more meticulous than you and his many of critics give him credit for.

bigbang said: Raven says: “The edge of evolution is known for now. Just look around. We are it. So is my cat.” . No no raven, he actual issue is just the edge of evolution via random mutations and selection. Understand? Why can’t you people seem to remember that? Or are you just being disingenuous?

bigbang said: Most everyone accepts, except perhaps raven’s straw man “creo,” which obviously neither Behe nor or I are, that life evolves, or unfolds as it were; and also in the reality of common descent.

I mean, if random mutation isn’t supposed to work as Behe claims, then how come random mutation is strongly implicated in the rise of so many novel genes, including nylonase, “antifreeze glycoprotein, and de-regulation of human lactase?

Arthur Hunt May 1, 2007 On the evolution of irreducible complexity http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html#more "The origins of the cmsT locus are fascinating. Several years ago, this locus was cloned and sequenced, and the sequence compared with normal maize mitochondrial DNA. This analysis revealed that the T-urf13 locus was the product of numerous recombination events (as many as seven different ones; along with reference 4, reference 6 has a nice overview of this). The consequence of these recombination events was the cobbling together of a number of disparate mitochondrial DNA (mtDNA) segments (I have tried to illustrate their origins in Figure 1) to yield a novel DNA segment in the cmsT mitochondrial genome. ———————————-" "The bottom line is that T-urf13 is a new protein, encoded by a gene that has no protein-coding antecedents; it is, bluntly, a new protein that arose “from scratch”, through a series of duplications, recombinations, and other mutations that occurred spontaneously in the course of the breeding process that gave rise to the cmsT line. These points are already problematic for the assertion by ID proponents that new protein-coding information cannot arise by natural processes. But T-urf13 is more than a nondescript polypeptide that happens to affect male fertility in corn. It turns out that T-urf13 is a membrane protein, and in membranes it forms oligomeric structures (I am not sure if the stoichiometries have been firmly established, but that it is oligomeric is not in question). This is the first biochemical trait I would ask readers to file away – this protein is capable of protein-protein interactions, between like subunits. This means that the T-urf13 polypeptide must possess interfaces that mediate protein-protein interactions. (Readers may recall Behe and Snokes, who argued that such interfaces are very unlikely to occur by chance.) T-urf13 also binds to the toxin produced by the fungal pathogen. But it does not just bind the toxin “passively” – upon binding, a non-selective ion channel is opened, leading to dissipation of transmembrane ion gradients, and all of the resulting events that accompany collapse of proton-motive force. (In mitochondria, this will lead to uncoupling and crippling of mitochondrial function; this is probably why cmsT plants are so devastated by the disease.) This is the second biochemical trait that readers should keep fresh in their minds – T-urf13 is a gated ion channel. (This an the other interesting biochemical properties of Turf13 are reviewed in reference 7.)"

2.) The environment is the totality of physical factors which causes differential reproductive success in a population of organisms Then you haven’t really specified what it is exactly that is causing the reproductive success. It is essentially a tautology.

So in most cases of evolution we must assume that something in the environment was causing the evolution, but as to exactly what it was, we don’t know and probably can never know.

Haeckyls embryos and pepperred moths are not in text books for historical effect they are presented as evidence for adaptations and common ancestry. I will admit that ID is not scientific if you admit the theory of evolution is not scientific. I mean, you can't get anymore scientific than aliens seeding the earth! Go panspermia and mutations!!

marv said: Haeckyls embryos and pepperred moths are not in text books for historical effect they are presented as evidence for adaptations and common ancestry. I will admit that ID is not scientific if you admit the theory of evolution is not scientific. I mean, you can't get anymore scientific than aliens seeding the earth! Go panspermia and mutations!!

marv said: I will admit that ID is not scientific if you admit the theory of evolution is not scientific.

I mean, you can't get anymore scientific than aliens seeding the earth! Go panspermia and mutations!!

Yes, Larry Boy, I picked that up, thanks. From what I can glean, the question remains open to some conjecture, although I believe I am correct in asserting that information blurring is happening through mutation- like events.

Torbjörn Larsson, OM said: What is "secular evolution"? Evolution is the same science for religious as atheist scientists.

Secular evolution is defined as slow, steady evolution. In galaxies, such evolution is either the result of long-term interactions between the galaxy and its environment (such as gas accretion or galaxy harassment), or it is induced by internal processes such as the actions of spiral arms or bars.

If I was a junior high student, I would have the sense enough to know aliens didn't put life on this planet. You do!!!! Go Panspermia! Science Rules. Richard Dawkins was right. Go mutations!!! Do an IP check and call me names instead of trying to defend your foolish theory that we are all mutated aliens.

We are mutated aliens. The eye is a simple mechanism. The first cell could have easily appeared because electricity and water when mixed always produces life. Plus Stanley Miller made some yellow gunk with an atmosphere exactly* like early earth. The universe is not a closed system. IDers are morons! There do I fit in yet?

To Tom Marking: A multidimensional space cannot be visualized, but it can be dealt with mathematically. Multidimensional space is common in various fields of physics and math, despite being not visualized, and many problems, some of an applied utility, are solved accounting for multidimensionality. Descending from a local peak (or saddle) into a shallow depression in the fitness landscape not necessarily results in the mutation that caused it being weeded out; it may be preserved if the drop is not very drastic, especially if the landscape co-evolves (as they routinely do) in a manner decreasing the selection pressure associated with the dimension in which the fitness drop took place. (The "dimensions" are in fact various features possessed by an organism which affect fitness. For example, an organism's fitness may be affected, say, by organism's hearing ability, sharpness of vision, and, say, its size. In such a scenario the fitness function is a function of three arguments, representing the listed features, so we deal here with a three-dimensional landscape. (In biological reality the number of dimensions is much larger of course). In each of those dimensions the fitness function may reach local peaks at different positions for each dimension, hence having saddles instead of real peaks.

For example, if the hearing ability drops because of a mutation, but at the same time the population of predators the escape from which requires a good hearing also decreased, thus alleviating the selection pressure causing the upward evolution of hearing, then the drop in hearing may not be disastrous, and the unfortunate mutation may survive, as evolution picks up in other dimension (say, improving vision).

It is very hard to get one’s mind around what a “saddle shape” is in 10,000 dimensions. I have a hard time visualizing that.

— Tom Marking

Behe, back when he did actual science, seems to have been a purified enzyme kind of guy

— trrll

Well, no Spiker, not exactly. Let me splain it again—-what we observe is that although it’s fairly clear that life has and continues to evolve, and that there’s plenty of evidence for common descent, it’s just that evolution by random mutation and selection is obviously quite limited.

— bigbang

...it just doesn’t really, in any meaningful and coherent way, truly explain most of the evolution of say flagellum, or the complexity of eukaryotic cells, or sentient beings.

— bigbang

...so really it’s just a matter of degree, isn’t it?

— bigbang

Except of course for the neo-Darwinian atheists that see no design whatsoever, but rather see only randomness and accidents, and, I suppose, what Dawkins what has hailed the non-random force of natural selection.

...it just that selection is circular and that we can’t really predict anything terribly specific, except the obvious, that the fittest traits survive.

— bigbang

marv said: Haeckyls embryos and pepperred moths are not in text books for historical effect they are presented as evidence for adaptations and common ancestry. I will admit that ID is not scientific if you admit the theory of evolution is not scientific. I mean, you can't get anymore scientific than aliens seeding the earth! Go panspermia and mutations!!

"" Finally, if the power of selection acting on heritable variation were “limited”, there would need to be some kind of mechanism or process that limits it. What could that be? ""

This seems to be a burden of proof issue. The Darwinists claim there is no limitation and also say they do not need to prove there is no limitation.

Most progressions in physics and chemistry have limits if not all. And biology has many limits. A dog cannot grow to 100 feet tall and an ant cannot become even one meter tall. The universe itself has limits. The natural world is full of limits. For Darwinism to exempt itself from the overwhelming probability that there are limits to what natural selection can do goes against all precedents.

Nigel asks: “If there were such a thing as a zoologist with no prior knowledge of dogs, how many species of dog would that person define? 50? 100? I have no idea….”

.

How many species? Well let’s see . . . hmmmm, since they’re all canines . . . yeah, it’d be just one: canines, wolves through shiatsus; but no felines . . . even artificial selection, helped by a random mutation here and there, has its limits, doesn’t it?

This is so very funny! To what lengths will people go to show that the bacterial flagelum does not look like a human made machine. Come on guys, we are talking about a God made machine. clearly we expect it to be many times more sophisticated and efficient (it is!). Yes it certainly does resemble a motor in it's structure, but this self assembling motor is an awesome design. Just face it...God rocks when it comes to building motors!

bobby said: "" Finally, if the power of selection acting on heritable variation were “limited”, there would need to be some kind of mechanism or process that limits it. What could that be? "" This seems to be a burden of proof issue. The Darwinists claim there is no limitation and also say they do not need to prove there is no limitation. Most progressions in physics and chemistry have limits if not all. And biology has many limits. A dog cannot grow to 100 feet tall and an ant cannot become even one meter tall. The universe itself has limits. The natural world is full of limits. For Darwinism to exempt itself from the overwhelming probability that there are limits to what natural selection can do goes against all precedents.

Stanton asks: Then how come Behe has not been able to explain why scientists have been able to observe the appearance of two different forms of the enzyme nylonase in two different species of bacteria, as well as document the origin and subsequent, repeated mutation of the “antifreeze” glycoprotein genes in Antarctic icefish as they colonized the coastal waters of Antarctica?

.

Well Stanton, as it turns out, Behe discusses this example of random mutation and selection at some length, if only you had read his book. Read pg 77 through 83 of EoE at your local B&N. Briefly, it turns out that the “antifreeze” protein is not a discrete structure comparable to say hemoglobin. The antifreeze protein is coded by multiple genes of different lengths all of which produce amino acid chains that get chopped into smaller fragments of differing length, kind of like the junk you’d find in your gutter (if you had a house and gutters); and unlike say hemoglobin and most other proteins that are coded by single genes.

bigbang said: Stanton asks: Then how come Behe has not been able to explain why scientists have been able to observe the appearance of two different forms of the enzyme nylonase in two different species of bacteria, as well as document the origin and subsequent, repeated mutation of the “antifreeze” glycoprotein genes in Antarctic icefish as they colonized the coastal waters of Antarctica? . Well Stanton, as it turns out, Behe discusses this example of random mutation and selection at some length, if only you had read his book. Read pg 77 through 83 of EoE at your local B&N. Briefly, it turns out that the “antifreeze” protein is not a discrete structure comparable to say hemoglobin. The antifreeze protein is coded by multiple genes of different lengths all of which produce amino acid chains that get chopped into smaller fragments of differing length, kind of like the junk you’d find in your gutter (if you had a house and gutters); and unlike say hemoglobin and most other proteins that are coded by single genes.

Let me explain why in this case Newton’s 2nd Law is not tautological. In a nutshell, the methodology for measuring F, M, and A are all different. F is measured with a spring, M is measured with a balance using standard weights, and A can be measured by looking at the motion of the object in question.

bigbang,

Hemoglobin is not coded for by a single gene. If Behe claimed this then he was simply wrong again. His ideas have no scientific merit whatsoever. Apparently the man refuses to even read the appropriate scientific literture but instead chooses to quote mine and misrepresent. He won't even admit it when he is caught in obvious mistake and shown conclusively to be wrong. You can stick with a sinking ship if you want, but Behe has lost whatever shred of scientific respectability he ever had in the scientific commmunity.

bigbang said: Nigel asks: “If there were such a thing as a zoologist with no prior knowledge of dogs, how many species of dog would that person define? 50? 100? I have no idea….” . How many species? Well let’s see . . . hmmmm, since they’re all canines . . . yeah, it’d be just one: canines, wolves through shiatsus; but no felines . . . even artificial selection, helped by a random mutation here and there, has its limits, doesn’t it?

Dolly Sheriff said: This is so very funny! To what lengths will people go to show that the bacterial flagelum does not look like a human made machine. Come on guys, we are talking about a God made machine. clearly we expect it to be many times more sophisticated and efficient (it is!). Yes it certainly does resemble a motor in it's structure, but this self assembling motor is an awesome design. Just face it...God rocks when it comes to building motors!

Cultist channeling Behe the idiot: Well Stanton, as it turns out, Behe discusses this example of random mutation and selection at some length, if only you had read his book. Read pg 77 through 83 of EoE at your local B&N. Briefly, it turns out that the “antifreeze” protein is not a discrete structure comparable to say hemoglobin. The antifreeze protein is coded by multiple genes of different lengths all of which produce amino acid chains that get chopped into smaller fragments of differing length, kind of like the junk you’d find in your gutter (if you had a house and gutters); and unlike say hemoglobin and most other proteins that are coded by single genes.

wikipedia: Gower 1 (ζ2ε2) Gower 2 (α2ε2) (PDB 1A9W) Hemoglobin Portland (ζ2γ2) In the fetus: Hemoglobin F (α2γ2) (PDB 1FDH) In adults: Hemoglobin A (α2β2) (PDB 1BZ0) - The most common with a normal amount over 95% Hemoglobin A2 (α2δ2) - δ chain synthesis begins late in the third trimester and in adults, it has a normal range of 1.5-3.5% Hemoglobin F (α2γ2) - In adults Hemoglobin F is restricted to a limited population of red cells called F-cells. However, the level of Hb F can be elevated in persons with sickle-cell disease

J Virol. 2004 Aug;78(15):8219-28. Links Characterization of the murine alpha interferon gene family.van Pesch V, Lanaya H, Renauld JC, Michiels T. University of Louvain, Christian de Duve Institute of Cellular Pathology, MIPA-VIRO 74-49, B-1200 Brussels, Belgium. Mouse and human genomes carry more than a dozen genes coding for closely related alpha interferon (IFN-alpha) subtypes. IFN-alpha, as well as IFN-beta, IFN-kappa, IFN-epsilon, and limitin, are thought to bind the same receptor, raising the question of whether different IFN subtypes possess specific functions. As some confusion existed in the identity and characteristics of mouse IFN-alpha subtypes, the availability of data from the mouse genome sequence prompted us to characterize the murine IFN-alpha family. A total of 14 IFN-alpha genes were detected in the mouse genome, in addition to three IFN-alpha pseudogenes. Four IFN-alpha genes (IFN-alpha1, IFN-alpha7/10, IFN-alpha8/6, and IFN-alpha11) exhibited surprising allelic divergence between 129/Sv and C57BL/6 mice. All IFN-alpha subtypes were found to be stable at pH 2 and to exhibit antiviral activity. Interestingly, some IFN subtypes (IFN-alpha4, IFN-alpha11, IFN-alpha12, IFN-beta, and limitin) showed higher biological activity levels than others, whereas IFN-alpha7/10 exhibited lower activity. Most murine IFN-alpha turned out to be N-glycosylated. However, no correlation was found between N-glycosylation and activity. The various IFN-alpha subtypes displayed a good correlation between their antiviral and antiproliferative potencies, suggesting that IFN-alpha subtypes did not diverge primarily to acquire specific biological activities but probably evolved to acquire specific expression patterns. In L929 cells, IFN genes activated in response to poly(I*C) transfection or to viral infection were, however, similar.

Behe is a lot more meticulous than you and his many of critics give him credit for.

— bigbang

Anything and everything (besides itself) that affects the reproductive success of the species.

Then you haven’t really specified what it is exactly that is causing the reproductive success. It is essentially a tautology.

Nigel D said: ...Therefore, your use of Behe as an authority in your argument makes your argument no stronger. Behe is a known liar.

Stanton says: “Hemoglobin is not coded for by a single gene.”

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Woops, I should have just said “unlike most other proteins that are coded by single genes [and added] that produce protein of definite length,” and left out the “hemoglobin.”

Of course hemoglobin, as everyone knows, is not actually a single protein chain, but rather a combination of separate proteins chains or subunits. The four chains of (adult) hemoglobin have two alpha and two beta chains. Then additionally you of course also have fetal hemoglobin which has two alpha chains and two gamma chains. And then of course there can be further complications like for some people who continue to make noticeable amounts of fetal hemoglobin throughout their lives----hereditary persistence of fetal hemoglobin, or HPFH. (People who have sickle cell disease and also often have milder clinical symptoms.) Thanks for helping me make that clear.

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Nigel says: “That’s why, after he claimed in EoE that HIV has not evolved any new biochemical interactions and blogger ERV (who works with HIV) called him out on his omission (HIV has evolved several new biochemical interactions since it became HIV), he tried to dismiss and discredit her rather than admit his error."

.

I think ERV may have been a bit bitchy and disrespectful, so maybe Behe ignored most of ERV’s crap. Still, Behe did acknowledge, in his back and forth with Musgrave, the development of a new viral protein-vial protein binding site that he now realizes he overlooked when writing EoE. In responding to Musgrave on this issue he noted (from Behe’s Amazon blog):

.

“One should, however, also make some distinctions with this example. First, although there apparently are five or so copies of Vpu in the viroporin complex, that does not mean that five binding sites developed. Only one new binding site need develop for one area of a protein which binds to a different area of the same protein, to form a homogeneous complex with, say, C5 symmetry. That is all that is required for a circularly symmetric structure to form. Second, the viroporin is not some new molecular machine. There is no evidence that it exerts its effect in, say, an ATP- or energy-dependent manner. Rather, similar to other viroporins, the protein simply forms a passive leaky pore or weak channel. (4,5) This situation is probably best viewed as a foreign protein degrading the integrity of a membrane, rather than performing some positive function.”

.

“And third, I explicitly pointed out in Chapter 8 of The Edge of Evolution that HIV had undergone enough mutating in past decades to form all possible viral-viral binding sites, but commented that apparently none of them had been helpful (now I know that one of them helped). This I discussed as the “principle of restricted choice””

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“A third reason for doubt is the overlooked problem of restricted choice. That is, not only do new protein interactions have to develop, there has to be some protein available that would actually do some good. Malaria makes about 5,300 kinds of proteins. Of those only a very few help in its fight against antibiotics, and just two are effective against chloroquine. If those two proteins weren’t available or weren’t helpful, then, much to the joy of humanity, the malarial parasite might have no effective evolutionary response to chloroquine. Similarly, in its frantic mutating, HIV has almost certainly altered its proteins at one point or another in the past few decades enough to cover all of shape space. So new surfaces on HIV proteins would have been made that could bind to any other viral protein in every orientation. [Emphasis added here.] Yet of all the many molecules its mutated proteins must have bound, none seem to have helped it; no new protein-protein interactions have been reported. Apparently the choice of proteins to bind is restricted only to unhelpful ones. (pp. 157-158)”

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“So Dr. Musgrave’s “core argument” turns out to be a decidedly double-edged sword. Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane. However, in the past fifty years many, many more potential viral protein-viral protein interactions must have also developed but not been selected because they did the virus little good. That is “restricted choice,” a very large contributor to the edge of evolution.”

"To be honest, I’m not sure how the existence of cheetahs makes gazelle evolution teleological, or why that’s even important. If natural selection fits someone’s definition of teleological, does the theory suddenly become wrong?"

There is perhaps some confusion in the use of the term teleology in this case. Perhaps the Darwinists and myself are using the term in different senses. I agree that there is no global teleology happening, no outside designer whose purpose is driving the system in some particular direction. But that does not mean that the individual components of the system are not themselves teleological.

When a cheetah crouches in the tall grass and waits for a gazelle to wander near enough, the cheetah has a plan to hide itself, wait for an opportune moment, and then pounce in order to catch the prey. The cheetah's behavior is teleological in the sense that certain prior behaviors are done in order to achieve some final goal (i.e., eating the gazelle). Such teleological behavior acts as selection on the prey species. So in that sense evolution involves teleology. If this was not the sense in which Darwin and evolutionists use the word, if they are only talking about global teleology, then pardon my ignorance, I withdraw the comment.

"Something looks designed. So what? Snowflakes look designed; that cloud from your childhood that looked like a unicorn looks designed."

A snowflake looks designed.
It's not.

A quartz crystal looks designed.
It's not.

A pocket watch looks designed.
It is.

I'm not sure how that arguments helps us. Some things that look designed are not really, and other things that look designed really are. How do we tell the difference?

"The population tends to spread out, both because of mutation, and because there are advantages to diversity within the population (not competing exactly with your neighbors for the same resources, not having the exact same vulnerability to diseases and parasites). So there is an outward pressure balancing the selective pressure toward the optimum, preventing all of the population from collapsing into a single genotype. This will push some of the population into the valley"

O.K. I got it. It's not strictly hill climbing because it's a cluster of points. The points are behaving in different ways throughout time and they are not synchronized with one another. I think I have a clearer picture now. Thanks.

But one thought does occur to me concerning this model. We can imagine the cluster of points separating into two clusters with perhaps each cluster climbing a different local peak. That's a representation of speciation in this model.

But in this model if we assume that the fitness landscape is changing then what happens when the two local maxima merge into the same point? Won't the separate species now merge together into one species? Why don't we see this happening in nature?

"What is “secular evolution”? Evolution is the same science for religious as atheist scientists."

http://dictionary.reference.com/browse/secular
sec·u·lar
Pronunciation[sek-yuh-ler]

–adjective
1. of or pertaining to worldly things or to things that are not regarded as religious, spiritual, or sacred; temporal: secular interests.
2. not pertaining to or connected with religion (opposed to sacred): secular music.
3. (of education, a school, etc.) concerned with nonreligious subjects.
4. (of members of the clergy) not belonging to a religious order; not bound by monastic vows (opposed to regular).
5. occurring or celebrated once in an age or century: the secular games of Rome.
6. going on from age to age; continuing through long ages.

–noun
7. a layperson.
8. one of the secular clergy.

I believe you were using definition #2 and I was using definition #6. LOL.

"It seems to be an astronomy term."

Sorry for the confusion. Scratch "secular evolution" and replace it with "long-term ongoing evolution". That's what I meant.

For all my new friends here at PT, here’s the latest post, 5/9/2008, by Behe, regarding malaria and mutations, from his Amazon blog------

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An interesting paper appeared recently in the New England Journal of Medicine. (1) The workers there discovered some new mutations which confer some resistance to malaria on human blood cells in the lab. (Their usefulness in nature has not yet been nailed down.) The relevance to my analysis in The Edge of Evolution is that, like other mutations that help with malaria, these mutations, too, are ones which degrade the function of a normally very useful protein, called pyruvate kinase. As the workers note:

"[H]eterozygosity for partial or complete loss-of-function alleles . . . may have little negative effect on overall fitness (including transmission of mutant alleles), while providing a modest but significant protective effect against malaria. Although speculative, this situation would be similar to that proposed for hemoglobinopathies (sickle cell and both -thalassemia and -thalassemia) and G6PD deficiency. . ."

This conclusion supports several strong themes of The Edge of Evolution which reviewers have shied away from. First, that even beneficial mutations are very often degradative mutations. Second, it’s a lot faster to get a beneficial effect (if one is available to be had) by degrading a gene than by making specific changes in genes. The reason is that there are generally hundreds or thousands of ways to break a gene, but just a few to alter it beneficially without degrading it. And third, that random mutation plus natural selection is incoherent. That is, separate mutations are often scattered; they do not add up in a systematic way to give new, interacting molecular machinery.

Even in the professional literature, sickle cell disease is still called, along with other mutations related to malaria, “one of the best examples of natural selection acting on the human genome.” (2) So these are our best examples! Yet breaking pyruvate kinase or G6PD or globin genes in thalassemia does not add up to any new system. Then where do the elegant nanosystems found in the cell come from? Not from random mutation and natural selection, that’s for sure.

1. Ayi, K., et al. 2008. Pyruvate kinase deficiency and malaria. N. Engl. J. Med. 358:1805-1810.

2. Tishkoff, S.A., et al. 2001. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293:455-462.

When a cheetah crouches in the tall grass and waits for a gazelle to wander near enough, the cheetah has a plan to hide itself, wait for an opportune moment, and then pounce in order to catch the prey. The cheetah’s behavior is teleological in the sense that certain prior behaviors are done in order to achieve some final goal (i.e., eating the gazelle).

When a cheetah crouches in the tall grass and waits for a gazelle to wander near enough, the cheetah has a plan to hide itself, wait for an opportune moment, and then pounce in order to catch the prey.

bobby said: "" Finally, if the power of selection acting on heritable variation were “limited”, there would need to be some kind of mechanism or process that limits it. What could that be? "" This seems to be a burden of proof issue. The Darwinists claim there is no limitation and also say they do not need to prove there is no limitation. Most progressions in physics and chemistry have limits if not all. And biology has many limits. A dog cannot grow to 100 feet tall and an ant cannot become even one meter tall. The universe itself has limits. The natural world is full of limits. For Darwinism to exempt itself from the overwhelming probability that there are limits to what natural selection can do goes against all precedents.

bigbang said: Nigel asks: “If there were such a thing as a zoologist with no prior knowledge of dogs, how many species of dog would that person define? 50? 100? I have no idea….” . How many species? Well let’s see . . . hmmmm, since they’re all canines . . . yeah, it’d be just one: canines, wolves through shiatsus; but no felines . . . even artificial selection, helped by a random mutation here and there, has its limits, doesn’t it?

Dolly Sheriff said: This is so very funny! To what lengths will people go to show that the bacterial flagelum does not look like a human made machine. Come on guys, we are talking about a God made machine. clearly we expect it to be many times more sophisticated and efficient (it is!). Yes it certainly does resemble a motor in it's structure, but this self assembling motor is an awesome design. Just face it...God rocks when it comes to building motors!

Tom Markin asks: “Some things that look designed are not really, and other things that look designed really are. How do we tell the difference?”

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The neo-Darwinian view would be that ultimately everything is the result of undirected random mutations and selection . . . or possibly, OTOH, as neo-Darwinian uber-atheist Dawkins recently opined when explaining evolution to Ben Stein, space aliens

"It is clear that a cheetah doesn’t necessarily have to have a plan to catch gazelles."

Well, you can replace this example with a human hunter sneaking up on a deer in order to shoot it. We know in this case the behavior is 100% teleological. How? By asking the hunter. Q: Hey, Joe, why were you hiding behind the tree and aiming your rifle? A: Because I had a plan. I intended to kill the deer.

And if you've watched any of the National Geographic specials about Jane Goodall and the chimpanzees at Gombe it seems pretty clear that our closest primate relatives also exhibit teleological hunting behaviors.

bigbang said: Stanton asks: Then how come Behe has not been able to explain why scientists have been able to observe the appearance of two different forms of the enzyme nylonase in two different species of bacteria, as well as document the origin and subsequent, repeated mutation of the “antifreeze” glycoprotein genes in Antarctic icefish as they colonized the coastal waters of Antarctica? . Well Stanton, as it turns out, Behe discusses this example of random mutation and selection at some length, if only you had read his book. Read pg 77 through 83 of EoE at your local B&N. Briefly, it turns out that the “antifreeze” protein is not a discrete structure comparable to say hemoglobin. The antifreeze protein is coded by multiple genes of different lengths all of which produce amino acid chains that get chopped into smaller fragments of differing length, kind of like the junk you’d find in your gutter (if you had a house and gutters); and unlike say hemoglobin and most other proteins that are coded by single genes.

Nigel explains: “Way to miss the point, bigbang.... Different breeds of dogs are very different from one another. So different that a zoologist who did not already know that they were the same species would almost certainly identify them as a great many different species….”

.

Oh, I see, you mean a zoologist like Dawkins. Well, in that case, he’d probably suggest that space aliens may have been responsible.

bigbang said: Nigel asks: “If there were such a thing as a zoologist with no prior knowledge of dogs, how many species of dog would that person define? 50? 100? I have no idea….” . How many species? Well let’s see . . . hmmmm, since they’re all canines . . . yeah, it’d be just one: canines, wolves through shiatsus; but no felines . . . even artificial selection, helped by a random mutation here and there, has its limits, doesn’t it?

If there were such a thing as a zoologist with no prior knowledge of dogs, how many species of dog would that person define? 50? 100? I have no idea, but it is far from obvious that dogs are one species, because their morphological variation is so vast.

— Nigel D

Nigel asks: “Does Behe even mention nylonase in EoE? Can he explain its origin in more than one form?”

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Sounds like essentially just more evidence of common descent. Behe never argues against common descent. He’s always been a believer in common descent as far as I know.

I think ERV may have been a bit bitchy and disrespectful, so maybe Behe ignored most of ERV’s crap.

— bigbang

Still, Behe did acknowledge, in his back and forth with Musgrave, the development of a new viral protein-vial protein binding site that he now realizes he overlooked when writing EoE. In responding to Musgrave on this issue he noted (from Behe’s Amazon blog):

Tom Marking said: "Something looks designed. So what? Snowflakes look designed; that cloud from your childhood that looked like a unicorn looks designed." A snowflake looks designed. It's not. A quartz crystal looks designed. It's not. A pocket watch looks designed. It is. I'm not sure how that arguments helps us. Some things that look designed are not really, and other things that look designed really are. How do we tell the difference?

"However, in the case of biological evolution, the observed natural processes are quite sufficient to bring about the amount of change that is recorded in the fossil record"

Just taking one lineage (i.e., horses) as an example:

Hyracotherium (early Eocene)
Mesohippus (Oligocene)
Mercyhippus (Miocene)
Pliohippus (Pliocene)
Equus (Pleistocene and Holocene)

What "observed natural processes" explain the evolution of Hyracotherium with a height of only 40 cm to modern horses with a height of 1.6m ? Where were these natural processes observed? Are they part of the fossil record itself?

" in the case of the watch, the materials from which it is made, and the shapes that its parts form are all familiar to many of us as designed and manufactured objects "

so only object which we know are designed can be designated as designed?

that is circular logic.

if an object fall to earth from space how can we analyze it to determine if it was designed?

But in this model if we assume that the fitness landscape is changing then what happens when the two local maxima merge into the same point? Won’t the separate species now merge together into one species? Why don’t we see this happening in nature?

— Tom Marking

bigbang said: Nigel explains: “Way to miss the point, bigbang.... Different breeds of dogs are very different from one another. So different that a zoologist who did not already know that they were the same species would almost certainly identify them as a great many different species….” Oh, I see, you mean a zoologist like Dawkins. Well, in that case, he’d probably suggest that space aliens may have been responsible.

bigbang said: For all my new friends here at PT, here’s the latest post, 5/9/2008, by Behe, regarding malaria and mutations, from his Amazon blog------ [IP infringing material deleted]

The neo-Darwinian view would be that ultimately everything is the result of undirected random mutations and selection … or possibly, OTOH, as neo-Darwinian uber-atheist Dawkins recently opined when explaining evolution to Ben Stein, space aliens

— bigbang

bigbang said: Nigel asks: “Does Behe even mention nylonase in EoE? Can he explain its origin in more than one form?” . Sounds like essentially just more evidence of common descent. Behe never argues against common descent. He’s always been a believer in common descent as far as I know.

"When two species are then brought together once more, if they cannot interbreed but still compete for resources"

Why can't the organisms from the two groups interbreed if the two groups are occupying the same region of phenotype (or perhaps genotype) space? They should be able to interbreed again if their genotypes are similar.

I think I'm getting confused by the model again. The clarity is slipping away once more. I thought I had it nailed down tight after the last explanation but apparently not.

Tom Marking said: "However, in the case of biological evolution, the observed natural processes are quite sufficient to bring about the amount of change that is recorded in the fossil record" Just taking one lineage (i.e., horses) as an example: Hyracotherium (early Eocene) Mesohippus (Oligocene) Mercyhippus (Miocene) Pliohippus (Pliocene) Equus (Pleistocene and Holocene) What "observed natural processes" explain the evolution of Hyracotherium with a height of only 40 cm to modern horses with a height of 1.6m ? Where were these natural processes observed? Are they part of the fossil record itself?

"Modern evolutionary theory (MET) contains several mechanisms of biological change. The theory has advanced somewhat in the last 140-odd years."

Can I get a complete enumeration of all of these mechanisms, and what the consensus estimate is from evolutionary biologists concerning the contribution of each to evolution. For example,

1.) natural selection - 80%
2.) genetic drift - 10%
3.) exaptation - 4%
4.) founder effect - 3%
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Or maybe no such list exists? I'd appreciate it if someone could point me to one. Thanks.

bobby said: " in the case of the watch, the materials from which it is made, and the shapes that its parts form are all familiar to many of us as designed and manufactured objects " so only object which we know are designed can be designated as designed? that is circular logic. if an object fall to earth from space how can we analyze it to determine if it was designed?

Tom Marking said: "When two species are then brought together once more, if they cannot interbreed but still compete for resources" Why can't the organisms from the two groups interbreed if the two groups are occupying the same region of phenotype (or perhaps genotype) space? They should be able to interbreed again if their genotypes are similar. I think I'm getting confused by the model again. The clarity is slipping away once more. I thought I had it nailed down tight after the last explanation but apparently not.

Tom Marking said: "When two species are then brought together once more, if they cannot interbreed but still compete for resources" Why can't the organisms from the two groups interbreed if the two groups are occupying the same region of phenotype (or perhaps genotype) space? They should be able to interbreed again if their genotypes are similar. I think I'm getting confused by the model again. The clarity is slipping away once more. I thought I had it nailed down tight after the last explanation but apparently not.

Tom Marking said: "Modern evolutionary theory (MET) contains several mechanisms of biological change. The theory has advanced somewhat in the last 140-odd years." Can I get a complete enumeration of all of these mechanisms, and what the consensus estimate is from evolutionary biologists concerning the contribution of each to evolution. For example, 1.) natural selection - 80% 2.) genetic drift - 10% 3.) exaptation - 4% 4.) founder effect - 3% . . . Or maybe no such list exists? I'd appreciate it if someone could point me to one. Thanks.

bobby said: " in the case of the watch, the materials from which it is made, and the shapes that its parts form are all familiar to many of us as designed and manufactured objects " so only object which we know are designed can be designated as designed? that is circular logic. if an object fall to earth from space how can we analyze it to determine if it was designed?

"These mechanisms include, but are not limited to, natural selection, genetic drift, sexual selection, recombination and random mutation. The examples of dogs and pigeons demonstrate the power of selection acting upon heritable variation to bring about change"

Wait a minute. Just so we're clear here. The observed mechanisms refer to observations on modern breeding of dogs and pigeons. These mechanisms are then applied to the fossil record, in this case, the evolution of horses. Is that what you're saying?

Actually, using this type of argument plays right into the hands of IDers and is therefore a terrible argument. It goes something like this:

1.) We can see remarkable changes produced by selection during breeding of dogs and pigeons by human beings
2.) We can see remarkable changes in the fossil record
3.) The selection during the breeding of dogs and pigeons is caused by a teleological agent (i.e., human beings)
4.) Therefore since the results are similar, the selection which resulted in the fossil record is also caused by a teleological agent (i.e., Intelligent Designer = God)

Nigel D said:

bobby said: " in the case of the watch, the materials from which it is made, and the shapes that its parts form are all familiar to many of us as designed and manufactured objects " so only object which we know are designed can be designated as designed? that is circular logic. if an object fall to earth from space how can we analyze it to determine if it was designed?

Bobby, get a grip. I said "e.g.". This is an abbreviation of exempla gratia which means "for example". It was an illustration of the point that we would need to apply additional knowledge to decide conclusively if an item were designed or not. For example, our knowledge of physics and chemistry, materials science, manufacturing processes and so forth. Your putative object-falling-from-the-sky would comprise some substance (or substances). If, for instance, one of these were steel, we would conclude that the object was manufactured, since steel does not occur naturally. Alternatively, if the object were covered in a metal foil of uniform thickness, we might conclude it was manufactured. Alternatively, if it were nickel, in a globular shape (which could be a natural object) but had obviious tool-marks on it, we would again conclude some form of manufacturing process. And so on. Note that the kind of evidence that we would find would be evidence that the object (like the watch) is manufactured, from which we could reasonably extrapolate to conclude some kind of design behind it. If, on the other hand, there were no evidence that the object had been manufactured, we could not conclude design. Either we would conclude that it was a natural object (i.e. formed by natural processes) or we would have to conclude that we simply didn't know. Science does not leap to conclusions - it requires firm evidence and logical inferences from the evidence. Without these, no scientific conclusions may be drawn.

"There is no consensus over the relative importance of the various mechanisms."

Since there is no consensus, how does anyone know that all the mechanisms have been discovered? How do you know that there aren't one or more unknown mechanisms contributing to evolution?

Since there is no consensus, how does anyone know that all the mechanisms have been discovered?

How do you know that there aren’t one or more unknown mechanisms contributing to evolution?

"We don’t know; but, since there is no evidence for other mechanisms, we know that we don’t know of other mechanisms."

If you could quantify the contributions of the various mechanisms that you do know then a missing mechanism would stick out like a sore thumb. For example:

natural selection - 60%
genetic drift - 10%
sexual selection - 10%
exaptation - 5%
founder effect - 5%
-------------------------
total - 90%

It's now obvious there's a missing 10% that cannot be explained by the existing mechanisms. But since evolution does not seem to be a very numerically precise theory I guess biologists will just have to stumble across new mechanisms more or less randomly.

"We don’t know; but, since there is no evidence for other mechanisms, we know that we don’t know of other mechanisms. Which is as close as science will get (since it can’t prove a universal negative)"

Which at this point goes into the realm of metaphysics and you are free to believe any entity you wish to believe, in case you want to believe in such a force teach it in a philosophy class because that doesn't concern science.

bigbang, we both have about 100-200 mutations from our parent and yet here we are, the nylon-eating bacteria is also a good example of "beneficial" mutations.

Actually an argument from design will favor the Raelians because we have not been "designed" very well and that should not be the case if the creator is "perfect", a lot of our features are jerry-rigged from fish, we can't make our own Vitamin C unlike other mammals and dolphins have non-functioning smelling gene that is only useful on land.

Actually, I like the fact that bigbang keep updating us with pseudoscience from Behe, bobby on the other hand is a troll

I’m not sure how that arguments helps us. Some things that look designed are not really, and other things that look designed really are. How do we tell the difference?

But in this model if we assume that the fitness landscape is changing then what happens when the two local maxima merge into the same point? Won’t the separate species now merge together into one species? Why don’t we see this happening in nature?

Tom Marking said: "These mechanisms include, but are not limited to, natural selection, genetic drift, sexual selection, recombination and random mutation. The examples of dogs and pigeons demonstrate the power of selection acting upon heritable variation to bring about change" Wait a minute. Just so we're clear here. The observed mechanisms refer to observations on modern breeding of dogs and pigeons. These mechanisms are then applied to the fossil record, in this case, the evolution of horses. Is that what you're saying? Actually, using this type of argument plays right into the hands of IDers and is therefore a terrible argument. It goes something like this: 1.) We can see remarkable changes produced by selection during breeding of dogs and pigeons by human beings 2.) We can see remarkable changes in the fossil record 3.) The selection during the breeding of dogs and pigeons is caused by a teleological agent (i.e., human beings) 4.) Therefore since the results are similar, the selection which resulted in the fossil record is also caused by a teleological agent (i.e., Intelligent Designer = God)

Tom Marking | May 15, 2008 1:37 PM | Reply “It is clear that a cheetah doesn’t necessarily have to have a plan to catch gazelles.” Well, you can replace this example with a human hunter sneaking up on a deer in order to shoot it. We know in this case the behavior is 100% teleological. How? By asking the hunter. Q: Hey, Joe, why were you hiding behind the tree and aiming your rifle? A: Because I had a plan. I intended to kill the deer. And if you’ve watched any of the National Geographic specials about Jane Goodall and the chimpanzees at Gombe it seems pretty clear that our closest primate relatives also exhibit teleological hunting behaviors.

Tom Marking said: "There is no consensus over the relative importance of the various mechanisms." Since there is no consensus, how does anyone know that all the mechanisms have been discovered? How do you know that there aren't one or more unknown mechanisms contributing to evolution?

Tom Marking said: If you could quantify the contributions of the various mechanisms that you do know then a missing mechanism would stick out like a sore thumb. For example: natural selection - 60% genetic drift - 10% sexual selection - 10% exaptation - 5% founder effect - 5% ------------------------- total - 90%

If you could quantify the contributions of the various mechanisms that you do know then a missing mechanism would stick out like a sore thumb. For example: natural selection - 60% genetic drift - 10% sexual selection - 10% exaptation - 5% founder effect - 5% ————————- total - 90% It’s now obvious there’s a missing 10% that cannot be explained by the existing mechanisms.

But since evolution does not seem to be a very numerically precise theory I guess biologists will just have to stumble across new mechanisms more or less randomly.

"whether evolution was teleological"

What does that mean? That's the heart of the issue. Clearly there are evolving beings (e.g., definitely humans, perhaps apes, perhaps other species) that are teleological. Does that make evolution teleological since it involves these organisms that are teleological?

I'm sure many folks on this blog have already heard of the Gaia hypthesis in which the entire biosphere adapts the planetary environment to suit itself which implies some level of teleology even if it is not conscious. I'm not sure I give that idea much credence but I'd be interested to hear what others have to say about it.

And if you’ve watched any of the National Geographic specials about Jane Goodall and the chimpanzees at Gombe it seems pretty clear that our closest primate relatives also exhibit teleological hunting behaviors.

“whether evolution was teleological” What does that mean? That’s the heart of the issue. Clearly there are evolving beings (e.g., definitely humans, perhaps apes, perhaps other species) that are teleological. Does that make evolution teleological since it involves these organisms that are teleological?

"How would you do this? Please design an experiment (or experiments) that would make this possible for any organism of your choice."

What the heck. You guys are the ones claiming you're observing these effects in pigeons, dogs, land snails, etc. You mean you can't quantify your observations of these effects (e.g., natural selection, genetic drift, etc.)? Why does it require a new experiment? This should be routine biological science.

Tom Marking said: The observed mechanisms refer to observations on modern breeding of dogs and pigeons. These mechanisms are then applied to the fossil record, in this case, the evolution of horses. Is that what you're saying? Actually, using this type of argument plays right into the hands of IDers and is therefore a terrible argument. It goes something like this: 1.) We can see remarkable changes produced by selection during breeding of dogs and pigeons by human beings 2.) We can see remarkable changes in the fossil record 3.) The selection during the breeding of dogs and pigeons is caused by a teleological agent (i.e., human beings) 4.) Therefore since the results are similar, the selection which resulted in the fossil record is also caused by a teleological agent (i.e., Intelligent Designer = God)

Nigel asks: "BTW, you did not answer my question. How come Behe cannot explain the origin of nylonases?"

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Apparently Behe considers it trivial. When asked if the independent evolution of nylonase in two different strains of flavobacterium and of pseudomonas aeruginosa was a good example of an increase of information in the genome; and whether it refuted the main contention of his book, Behe replied:

“No. Those enzymes are very simple ones which simply hydrolyze precursors to nylon. That’s a very simple task, which can be done even by small organic catalysts.”

.

You know Nigel, Behe’s EoE is now selling for only $7 at Amazon----you should order yourself a copy if for no other reason than to find and expose all the lies and poor scholarship that you and everyone else here is convinced that Behe is guilty of.

Contrary to your POV, I myself find Behe rather interesting, knowledgeable, likable, a very good writer and explainer of a rather difficult subject, a rebel of sorts; and I suppose I tend to like people capable of thoughtfully and intelligently bucking consensus. Seems to me he’s taken a lot of unnecessary abuse from the neo-Darwinan consensus crowd, and yet he’s generally rather calm and civil.

Anywho, since we now realize that the universe isn’t infinite and eternal after all, but rather that it did indeed have a beginning, a beginning with inexplicably low entropy; and since we now realize how finely tuned things seem to be; being an atheist is no longer as intellectually satisfying as it once was, whereas believing in first cause/design is. So I'm no longer an atheist and the question is how far down the design goes----I suppose that life and we sentient beings might still be an accident, or maybe a product of Dawkins’s space aliens, but I’m not yet convinced.

Nice chatting with everyone.
bigbang

Tom Marking said: "How would you do this? Please design an experiment (or experiments) that would make this possible for any organism of your choice." What the heck. You guys are the ones claiming you're observing these effects in pigeons, dogs, land snails, etc. You mean you can't quantify your observations of these effects (e.g., natural selection, genetic drift, etc.)? Why does it require a new experiment? This should be routine biological science.

"The arguments by Behe et al, re mousetraps and flagellums, is that such structures cannot be created step by step via random mutation and selection, period. Whence the selection comes makes no differece."

O.K. Thanks for the clarification. I guess you can tell I am not well versed in ID thinking nor in the works of Michael Behe. So are they claiming that even human beings using artificial selection could not produce the same result if they started from the same starting place?

What about if humans could assemble the same biological structure, atom by atom. Do they claim that there would be something preventing us from doing that? That only the Intelligent Designer can do it?

Tom Marking said: "How would you do this? Please design an experiment (or experiments) that would make this possible for any organism of your choice." What the heck. You guys are the ones claiming you're observing these effects in pigeons, dogs, land snails, etc. You mean you can't quantify your observations of these effects (e.g., natural selection, genetic drift, etc.)? Why does it require a new experiment? This should be routine biological science.

"Natural selection, genetic drift, etc can be observed and it is possible to say that in one situation one of these has been more important than another. However, as far as I know it is not possible to put even approximate figures for the relative importance of each. To begin with, exactly what would you be measuring?"

O.K. Let me propose an experiment, but I'm sure many, many biologists have thought of things like this before and probably much better.

1.) Genetic drift group - You put 1,000 Drosophila melanogaster in some type of enclosure which we call the reference environment. It has some standard amount of food and type of food. You let the population evolve. You do sampling every so often (maybe every day you pull out 10 at random and sample their genome). You see how the genome varies with time. This gives you some idea of genetic drift when there is no particular selection pressure being applied.

2.) Natural selection group - 1,000 Drosophila melanogaster in an enclosure of the same size. You slowly vary the type of food from let's say something sucrose-based to some other sugar that's harder to digest. You do the same sampling of the genome. This should give you some idea on how the genome is varying when the population is under stress and therefore undergoing selection.

And there could be various natural selection groups where you vary different aspects of the environment such as temperature, amount of food, etc., etc.

So that's the type of experiment I would run in order to get some idea on the relative importance of selection versus genetic drift. But I'm sure there are experts who have thought about this and have much better ideas for experiments.

"Intentional behavior on the part of some organisms does not imply that evolution of a species (theirs or another) was also intentional on the part of something else."

Let's perform a thought experiment, which sadly, is not too different from reality. Let's say Homo sapiens decided to drive into extinction all species of the class amphibians. To a certain extent this is already a real possibility but let's assume it became public policy. Is there any doubt that we couldn't achieve this goal?

Now, let's say humans go extinct and some other intelligent species evolves in our place millions of years from now. When that intelligent species' geologists examined the fossil record they would note a sudden dissapearance of the class amphibia in the fossil record. Such an evolutionary signature would be teleological and perhaps the intelligent species of the future would even be able to deduce that it was purposeful. So from their point of view certain aspects of evolutionary history would be teleological and others wouldn't be. It would be a mixture of the two. And all of this would be true even without an Intelligent Designer.

Has anyone else noticed that bobby's main purposes here seem to be

a) Promote Behe, i.e. he's much more meticulous... etc etc than you people give him credit for.

and

b) annoy everyone here by disrupting the actual science related discussions.

He offers a strange mixture of technobabble re Behe's "biochemistry" and a rather juvenile taunting behavior. He seems so familiar with Behe's work and so enamored of him that I'm beginning to wonder if bobby isn't actually Behe himself. If he isn't then he sure has an odd fixation on the man.

bigbang said: Oh, I see, you mean a zoologist like Dawkins. Well, in that case, he’d probably suggest that space aliens may have been responsible.

bigbang said: Nigel asks: "BTW, you did not answer my question. How come Behe cannot explain the origin of nylonases?" Apparently Behe considers it trivial. When asked if the independent evolution of nylonase in two different strains of flavobacterium and of pseudomonas aeruginosa was a good example of an increase of information in the genome; and whether it refuted the main contention of his book, Behe replied: “No. Those enzymes are very simple ones which simply hydrolyze precursors to nylon. That’s a very simple task, which can be done even by small organic catalysts.”

bigbang said: Seems to me [Behe]’s taken a lot of unnecessary abuse from the neo-Darwinan consensus crowd, and yet he’s generally rather calm and civil.

Anywho, since we now realize that the universe isn’t infinite and eternal after all, but rather that it did indeed have a beginning, a beginning with inexplicably low entropy; and since we now realize how finely tuned things seem to be; being an atheist is no longer as intellectually satisfying as it once was, whereas believing in first cause/design is.

I’m sure many folks on this blog have already heard of the Gaia hypthesis in which the entire biosphere adapts the planetary environment to suit itself which implies some level of teleology even if it is not conscious. I’m not sure I give that idea much credence but I’d be interested to hear what others have to say about it.

Tom Marking said: So are they claiming that even human beings using artificial selection could not produce the same result if they started from the same starting place?

What about if humans could assemble the same biological structure, atom by atom. Do they claim that there would be something preventing us from doing that? That only the Intelligent Designer can do it?

Tom Marking said: So from their point of view certain aspects of evolutionary history would be teleological and others wouldn't be. It would be a mixture of the two. And all of this would be true even without an Intelligent Designer.

1.) Genetic drift group - You put 1,000 Drosophila melanogaster in some type of enclosure which we call the reference environment. It has some standard amount of food and type of food. You let the population evolve. You do sampling every so often (maybe every day you pull out 10 at random and sample their genome). You see how the genome varies with time. This gives you some idea of genetic drift when there is no particular selection pressure being applied.

Tom Marking said: O.K. Let me propose an experiment, but I'm sure many, many biologists have thought of things like this before and probably much better. 1.) Genetic drift group - You put 1,000 Drosophila melanogaster in some type of enclosure which we call the reference environment. It has some standard amount of food and type of food. You let the population evolve. You do sampling every so often (maybe every day you pull out 10 at random and sample their genome). You see how the genome varies with time. This gives you some idea of genetic drift when there is no particular selection pressure being applied. 2.) Natural selection group - 1,000 Drosophila melanogaster in an enclosure of the same size. You slowly vary the type of food from let's say something sucrose-based to some other sugar that's harder to digest. You do the same sampling of the genome. This should give you some idea on how the genome is varying when the population is under stress and therefore undergoing selection.

GuyeFaux said: This highlights well the difficulty of doing such experiments:

1.) Genetic drift group - You put 1,000 Drosophila melanogaster in some type of enclosure which we call the reference environment. It has some standard amount of food and type of food. You let the population evolve. You do sampling every so often (maybe every day you pull out 10 at random and sample their genome). You see how the genome varies with time. This gives you some idea of genetic drift when there is no particular selection pressure being applied.

[emphasis mine]. The thing is, you haven't really removed selection for this group. For instance, even you provide a veritable fruit-fly paradise, you will still be selecting for those individuals who best thrive in this environment. For instance, you still haven't eliminated the selective pressure for quicker reproduction, ability to metabolize that particular kind of food, be attractive to other fruitflies, lay more eggs, take advantage of the lighting conditions, etc. A better way to ensure no selection is to randomly kill of a certain segment of the population every once in a while, but in that case you're still selecticting for individuals who can produce the most offspring in the shortest amount of time.

So I guess that would be an example of genetic draft.

David Stanton said: So I guess that would be an example of genetic draft.

"Time flies like the wind: Fruit flies like bananas"

"If species A wipes out species B, then that’s what it was. Evolution doesn’t care about the reason."

If that's true then why are we arguing at all? Why did Darwin spend 30 years of his life searching for a mechanism to explain evolution if the mechanism doesn't matter? You could have natural selection, Yahweh mucking around with DNA, the Flying Spaghetti Monster mucking around with DNA, etc., etc. and as long as the result is the same you say it doesn't matter?

Tom Marking said: "If species A wipes out species B, then that’s what it was. Evolution doesn’t care about the reason." If that's true then why are we arguing at all? Why did Darwin spend 30 years of his life searching for a mechanism to explain evolution if the mechanism doesn't matter? You could have natural selection, Yahweh mucking around with DNA, the Flying Spaghetti Monster mucking around with DNA, etc., etc. and as long as the result is the same you say it doesn't matter?

“If species A wipes out species B, then that’s what it was. Evolution doesn’t care about the reason.” If that’s true then why are we arguing at all? Why did Darwin spend 30 years of his life searching for a mechanism to explain evolution if the mechanism doesn’t matter?

Tom Marking said: "We don’t know; but, since there is no evidence for other mechanisms, we know that we don’t know of other mechanisms." If you could quantify the contributions of the various mechanisms that you do know then a missing mechanism would stick out like a sore thumb. For example: natural selection - 60% genetic drift - 10% sexual selection - 10% exaptation - 5% founder effect - 5% ------------------------- total - 90% It's now obvious there's a missing 10% that cannot be explained by the existing mechanisms. But since evolution does not seem to be a very numerically precise theory I guess biologists will just have to stumble across new mechanisms more or less randomly.

Now, let’s say humans go extinct and some other intelligent species evolves in our place millions of years from now. When that intelligent species’ geologists examined the fossil record they would note a sudden dissapearance of the class amphibia in the fossil record. Such an evolutionary signature would be teleological and perhaps the intelligent species of the future would even be able to deduce that it was purposeful. So from their point of view certain aspects of evolutionary history would be teleological and others wouldn’t be. It would be a mixture of the two. And all of this would be true even without an Intelligent Designer.

Oh, and before I forget: Tom, the thing that's killing off many, if not most frogs, besides acid rain, exotic predators and habitat destruction is a chrytid fungus. It turns out that this particular chrytid fungus is a disease of African clawed frogs, and because the clawed frogs were imported throughout the world for pregnancy tests (in that injecting a female clawed frog with urine of a pregnant woman induces it to lay eggs), so, too, was the fungus.

"WHAT? Darwin endeavored to explain a mechanism for development of species from earlier species; you’re talking about what might kill off a species. That’s not the same question."

So you appear to be arguing that the mechanism for the development of a species is important, but the mechanism for the extinction of a species is of no relevance. Great!, I can now go off and claim that natural selection explains the development of each species but it was the Flying Spaghetti Monster that caused all the extinctions.

"Second, IDers refuse to do any actual digging. Instead, they take the position that they’ve come up with such a good idea that it is not their responsibility to look for evidence."

That's because ID is a religious/political movement masquerading as science. The main battleground is educational policy. They could probably care less if any of their ideas were scientifically testable. Get over it and stop whinging about it.

Tom Marking said: "WHAT? Darwin endeavored to explain a mechanism for development of species from earlier species; you’re talking about what might kill off a species. That’s not the same question." So you appear to be arguing that the mechanism for the development of a species is important, but the mechanism for the extinction of a species is of no relevance. Great!, I can now go off and claim that natural selection explains the development of each species but it was the Flying Spaghetti Monster that caused all the extinctions.

Tom Marking said: "If species A wipes out species B, then that’s what it was. Evolution doesn’t care about the reason." If that's true then why are we arguing at all? Why did Darwin spend 30 years of his life searching for a mechanism to explain evolution if the mechanism doesn't matter? You could have natural selection, Yahweh mucking around with DNA, the Flying Spaghetti Monster mucking around with DNA, etc., etc. and as long as the result is the same you say it doesn't matter?

Tom Marking said: So you appear to be arguing that the mechanism for the development of a species is important, but the mechanism for the extinction of a species is of no relevance. Great!, I can now go off and claim that natural selection explains the development of each species but it was the Flying Spaghetti Monster that caused all the extinctions.

As Evo Devo Sean Carroll, Professor of Molecular Biology, Genetics, and Medical Genetics at the University of Wisconsin–Madison observed, in his Endless forms most beautiful, 2005: “The surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated he appearance of those bodies in the Cambrian Explosion. The genetic potential was in place for at least 50 million years, and probably a fair bit longer, before large, complex forms emerged.”

.

I think most neo-Darwinians would agree that this discovery----that all of the genes for building large, complex animal bodies were in place millions of years b/f those animal bodies even emerged----illustrates the power and reality of neo-Darwinian evolution by random mutation and natural selection. Leaving the neo-Darwinians wondering, in light of Sean Carroll’s observation, how anyone could possibly suggest that evolution by random mutation and natural selection is limited or an incomplete theory?

"" The surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated he appearance of those bodies in the Cambrian Explosion. ""

Then HOW did they get there??

Bobby asks: “Then HOW did they get there??”

.

RM + NS, how else? And that RM + NS did it b/f those animal bodies even emerged illustrates the power of the RM + NS; and is yet another reason that we can be so certain that RM & NS has to be true for all of evolution.

You're wasting your time bigbang, the question was rhetorical. All of Bobby's questions are rhetorical. Bobby knows all about evolution, including where genes come from. And even if he didn't, it has been explained to him many times already.

So you appear to be arguing that the mechanism for the development of a species is important, but the mechanism for the extinction of a species is of no relevance.

I think most neo-Darwinians would agree that this discovery—-that all of the genes for building large, complex animal bodies were in place millions of years b/f those animal bodies even emerged—-illustrates the power and reality of neo-Darwinian evolution by random mutation and natural selection.

Trrll says: "evolution of larger species is expected to be mostly tinkering–tweaks and recombination of sequence motifs that were invented by the little guys."

.

Bingo. And skeptics like Behe pretty much agree with the ability of RM + NS to tinker, and with common descent too----they just lack the faith in RM+NS’s ability to evolve all those genes, all the complex molecular machinery, required for building large, complex animal bodies millions of years b/f those animal bodies even emerged. And I think that’s Behe’s biggest problem----his lack of faith in what most neo-Darwinians know has to be true, in this case that RM+NS evolved all the genes, all the complex molecular machinery, required for building large, complex animal bodies millions of years b/f those animal bodies even emerged, (although, admittedly, Darwinism never predicted this b/f Evo-Devo discovered it), and why he believes that neo-Darwinian evolution by RM+NS is a limited and incomplete theory.

When you think about it, how could RM+NS not be true? I mean what could be more obvious than that the fittest traits would survive?

Trrll says: “Actually, I think that the theory [RM+NS] would be in trouble if this were not the case [that all the genes for building large, complex animal bodies were in place millions of years b/f those animal bodies even emerged]. Because of the smaller populations and longer generation times, evolution of larger species is expected to be mostly tinkering–tweaks and recombination of sequence motifs that were invented by the little guys.”

.

Sure, plus if those genes hadn’t been in place then we multi-cellular sentient beings wouldn’t even be here to declare that RM+NS did what it did . . . too bad Darwinian RM+NS didn’t predicted that b/f Evo-Devo discovered it, say like the Big Bang model predicted the CMBR b/f the CMBR was discovered. Still, no one can deny that RM+NS does at least predict simpler things like the evolution of drug resistance by various organisms/viruses.

Trrll says: “Actually, I think that the theory [RM+NS] would be in trouble if this were not the case [that all the genes for building large, complex animal bodies were in place millions of years b/f those animal bodies even emerged]. Because of the smaller populations and longer generation times, evolution of larger species is expected to be mostly tinkering–tweaks and recombination of sequence motifs that were invented by the little guys.”

.

Sure, plus if those genes hadn’t been in place then we multi-cellular sentient beings wouldn’t even be here to reveal that RM+NS did what it did . . . too bad Darwinian RM+NS didn’t predicted that b/f Evo-Devo discovered it, say like the Big Bang model predicted the CMBR b/f the CMBR was discovered. Still, no one can deny that RM+NS does at least predict simpler things like the evolution of drug resistance by various organisms/viruses.

Philip Bruce Heywood said: Nige, I know the human genome isn't changing. Torbjorn says it is - he says we are evolving, right now. Your reply was an improvement on Strife'sGrandmother's.

bigbang said: Sure, plus if those genes hadn’t been in place then we multi-cellular sentient beings wouldn’t even be here to reveal that RM+NS did what it did . . . too bad Darwinian RM+NS didn’t predicted that b/f Evo-Devo discovered it, say like the Big Bang model predicted the CMBR b/f the CMBR was discovered. Still, no one can deny that RM+NS does at least predict simpler things like the evolution of drug resistance by various organisms/viruses.

Stanton says: “Do also realize that the scientists back in Charles Darwin’s day were totally unaware of the existence of DNA and RNA, as well as being ignorant of the function of the genome.”

.

Well sure, but natural selection is still viewed as acting on an organism's physical characteristics, or phenotype; it’s just that we now know that phenotype is determined by an organism's genotype and that it’s random mutations to the DNA that provides much of the variation that NS then acts upon.

OTOH, based on the Evo-Devo discovery----that the genes required for building large, complex animal bodies, or phenotypes, were in place millions of years b/f those animal bodies, those phenotypes, even emerged----we can now see that NS somehow acted upon those phenotypes b/f they even emerged! Something that neither Darwin, nor any other Darwinian, would have foreseen.

bigbang said: what we observe is that although it’s fairly clear that life has and continues to evolve, and that there’s plenty of evidence for common descent, it’s just that evolution by random mutation and selection is obviously quite limited.

bigbang said: Larrson said: “And of course we know the bodies that move are the most energetic b/c if they weren’t, they’d not have moved. Circular perhaps, but undeniably a truism.” . You’re probably thinking of some sort of equation. Not that it matters but equations quantify the theories/natural laws that have been discovered by physicists which are then used to predict things; the terms on both sides of an equation are typically defined elsewhere; the equal sign does not mean "is defined by, " it means is equal to. Fitness, on the other hand is defined by selection-----see the difference?

bigbang said: Still, selection is not the issue; selection pressures seem to be undeniable; it just that selection is circular and that we can’t really predict anything terribly specific, except the obvious, that the fittest traits survive.

angst said: It seems to be an astronomy term. From the SAO Encyclopedia of Astronomy:

Secular evolution is defined as slow, steady evolution.

Larsson says: “Despite that you claim, that known mechanisms don’t explain evolution of observed traits, that is exactly what the current theory successfully does.”

.

I must be evolving Larsson b/c I now more or less agree with you----based on the Evo-Devo discovery that the genes required for building large, complex animal bodies, or phenotypes, were in place millions of years b/f those animal bodies, those phenotypes, even emerged----that somehow NS was able to select those phenotypes, those traits, obviously products of RM, b/c RM is all there ever was, is, or will be, b/f they even emerged. Now that I think about it, how could it be otherwise?

You say that “fitness isn’t defined by selection but by reproductive success.” Sure, I’ll go with that----and we know that a trait has reproductive success b/c if it didn’t it would not have been selected: ergo, reproductive success is defined by selection.

bigbang said: You say that “fitness isn’t defined by selection but by reproductive success.” Sure, I’ll go with that----and we know that a trait has reproductive success b/c if it didn’t it would not have been selected: ergo, reproductive success is defined by selection.

Tom Marking said: But in this model if we assume that the fitness landscape is changing then what happens when the two local maxima merge into the same point? Won't the separate species now merge together into one species? Why don't we see this happening in nature?

Tom Marking said: What "observed natural processes" explain the evolution of Hyracotherium with a height of only 40 cm to modern horses with a height of 1.6m ? Where were these natural processes observed? Are they part of the fossil record itself?

Tom Marking said: Actually, using this type of argument plays right into the hands of IDers and is therefore a terrible argument.

Tom Marking said: I think I'm getting confused by the model again. The clarity is slipping away once more. I thought I had it nailed down tight after the last explanation but apparently not.

bigbang said: I must be evolving Larsson b/c I now more or less agree with you----based on the Evo-Devo discovery that the genes required for building large, complex animal bodies, or phenotypes, were in place millions of years b/f those animal bodies, those phenotypes, even emerged----that somehow NS was able to select those phenotypes, those traits, obviously products of RM, b/c RM is all there ever was, is, or will be, b/f they even emerged. Now that I think about it, how could it be otherwise?

bigbang said: You say that “fitness isn’t defined by selection but by reproductive success.” Sure, I’ll go with that----and we know that a trait has reproductive success b/c if it didn’t it would not have been selected: ergo, reproductive success is defined by selection.

Tom Marking wrote:

"What “observed natural processes” explain the evolution of Hyracotherium with a height of only 40 cm to modern horses with a height of 1.6m ? Where were these natural processes observed? Are they part of the fossil record itself?"

Since the change required about 50 million years to occur there was obviously no direct observation of the selection pressures in this case. However, that does not mean that a scenario consistent with known facts cannot be deduced.

The classic explanation is that climate change induced a shift from browzing to grazing. This is consistent with climatological data and with the observed change in dentition within the equine lineage. This presumably lead to increased selection through predation which favored increased size and speed. The concommitant increase in size and the further reduction in toe number thus lead to a body type that was more capable of avoiding predation in the grassland environment. So today horses are large and run on the toenail of the middle digit.

There are a lot of intermediate fossils that reveal this pattern. There is a good summary of the topic in the Talk Origins archive if anyone is interested.

too bad Darwinian RM+NS didn’t predicted that b/f Evo-Devo discovered it

I must be evolving Larsson b/c I now more or less agree with you—-based on the Evo-Devo discovery that the genes required for building large, complex animal bodies, or phenotypes, were in place millions of years b/f those animal bodies, those phenotypes, even emerged—-that somehow NS was able to select those phenotypes, those traits, obviously products of RM, b/c RM is all there ever was, is, or will be, b/f they even emerged. Now that I think about it, how could it be otherwise?

Trrll says: “Because those protein and RNA sequence motifs were not initially selected for their ability to build large complex animal bodies, but rather for their versatility.”

.

Sure, in those ancient single cell organisms (close to 10^40 of them), b/f the Cambrian Explosion, NS must have been selecting randomly mutated sequence motifs for their versatility, which must have somehow conferred greater fitness then the lesser sequence motifs in those single cell organisms (b/c otherwise they’d not have been selected); and then, during the Cambrian Explosion, when all those versatile motifs could be used to build large complex animal bodies, NS could then select for fitness among the emerged animal bodies.

Sure, in those ancient single cell organisms (close to 10^40 of them), b/f the Cambrian Explosion, NS must have been selecting randomly mutated sequence motifs for their versatility, which must have somehow conferred greater fitness then the lesser sequence motifs in those single cell organisms (b/c otherwise they’d not have been selected); and then, during the Cambrian Explosion, when all those versatile motifs could be used to build large complex animal bodies, NS could then select for fitness among the emerged animal bodies.

Trrll says: "So when we look at large, multicellular creatures, we are necessarily looking at the descendants of those microorganisms that were not merely most capable of surviving, but also the most capable of evolving."

.

Sure, common descent (which even guys like Behe agrees with), and NS selecting for fitness and evolvability. As Evo-Devo has discovered, all of the essential evolution of the genes required to build and evolve those large complex animal bodies, albeit unexpectedly by neo-Darwinian thinking prior to the discovery, had already taken place in those ancient and relatively simple single cell organisms, close to 10^40 of them, prior to the Cambrian Explosion; paving the way for the emergence of the variety of multicellular creatures that we see (and are) today.

bigbang said: As Evo Devo Sean Carroll, Professor of Molecular Biology, Genetics, and Medical Genetics at the University of Wisconsin–Madison observed,

in his Endless forms most beautiful, 2005: “The surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated he appearance of those bodies in the Cambrian Explosion. The genetic potential was in place for at least 50 million years, and probably a fair bit longer, before large, complex forms emerged.” . I think most neo-Darwinians would agree that this discovery----that all of the genes for building large, complex animal bodies were in place millions of years b/f those animal bodies even emerged----illustrates the power and reality of neo-Darwinian evolution by random mutation and natural selection. Leaving the neo-Darwinians wondering, in light of Sean Carroll’s observation, how anyone could possibly suggest that evolution by random mutation and natural selection is limited or an incomplete theory?

bobby said: "" The surprising message from Evo Devo is that all of the genes for building large, complex animal bodies long predated he appearance of those bodies in the Cambrian Explosion. "" Then HOW did they get there??

Bingo. And skeptics like Behe

— bigbang

pretty much agree with the ability of RM + NS to tinker, and with common descent too—-they just lack the faith in RM+NS’s ability to evolve all those genes, all the complex molecular machinery, required for building large, complex animal bodies millions of years b/f those animal bodies even emerged.

And I think that’s Behe’s biggest problem—-his lack of faith in what most neo-Darwinians know has to be true, in this case that RM+NS evolved all the genes, all the complex molecular machinery, required for building large, complex animal bodies millions of years b/f those animal bodies even emerged, (although, admittedly, Darwinism never predicted this b/f Evo-Devo discovered it), and why he believes that neo-Darwinian evolution by RM+NS is a limited and incomplete theory.

When you think about it, how could RM+NS not be true? I mean what could be more obvious than that the fittest traits would survive?

bigbang said: Trrll says: "So when we look at large, multicellular creatures, we are necessarily looking at the descendants of those microorganisms that were not merely most capable of surviving, but also the most capable of evolving." . Sure, common descent (which even guys like Behe agrees with), and NS selecting for fitness and evolvability. As Evo-Devo has discovered, all of the essential evolution of the genes required to build and evolve those large complex animal bodies, albeit unexpectedly by neo-Darwinian thinking prior to the discovery, had already taken place in those ancient and relatively simple single cell organisms, close to 10^40 of them, prior to the Cambrian Explosion; paving the way for the emergence of the variety of multicellular creatures that we see (and are) today.

"the real observed flagella do not look like “machines” at all. In fact the structure of flagella is more typical of a bacteriophage virus" -- Mark Perakh

micrograph of flagella (sans motor proteins and extraction appratus)...
http://www.talkdesign.org/faqs/img/fig1.gif
(from website dedicated to "proving" argument from design is wrong)

micrograph of your "typical" bacteriophage virus...
http://www.biochem.wisc.edu/faculty/inman/empics/0021a.jpg

Who you trying to kid, Mark?!

I have no interest to "kid" the likes of whoever is cowardly enough to hide his/her real name (like "yonsaon" does). So, regardless of whether "yonsaon" chooses to reply to this comment or keeps silent, I'll not continue arguing with him/her.

Images of flagella and of a bacteriophage virus he/she referred to were made with insufficient magnifications to make them telling about the similarities between the two entities. The image of the flagellum on the talkorigin site was used more than once by the creos, so it tells nothing new, not known until now. Its resolution was insuffiient to see the details as could be discerned on the more recent images, like some of those shown in my post (which are just a small fraction of many such photos and reconstructions based on X-rays technique). Btw, "yonsaon's" expression "who are you kidding" is exactly what Dembski has used as a title of his pseudo-review of my book on Amazon. Isn't it a funny coincidence?

Intelligent evolution questioners have moved on to the equine flagellum. Its most paradigm-shattering trait is that it still functions after the death of the specimen.

Marion Delgado said: Intelligent evolution questioners have moved on to the equine flagellum. Its most paradigm-shattering trait is that it still functions after the death of the specimen.

yonsaon said: "the real observed flagella do not look like “machines” at all. In fact the structure of flagella is more typical of a bacteriophage virus" -- Mark Perakh micrograph of flagella (sans motor proteins and extraction appratus)... http://www.talkdesign.org/faqs/img/fig1.gif (from website dedicated to "proving" argument from design is wrong) micrograph of your "typical" bacteriophage virus... http://www.biochem.wisc.edu/faculty/inman/empics/0021a.jpg Who you trying to kid, Mark?!

Tom Marking said: "These mechanisms include, but are not limited to, natural selection, genetic drift, sexual selection, recombination and random mutation. The examples of dogs and pigeons demonstrate the power of selection acting upon heritable variation to bring about change" Wait a minute. Just so we're clear here. The observed mechanisms refer to observations on modern breeding of dogs and pigeons.

These mechanisms are then applied to the fossil record, in this case, the evolution of horses. Is that what you're saying?

Actually, using this type of argument plays right into the hands of IDers and is therefore a terrible argument. It goes something like this: 1.) We can see remarkable changes produced by selection during breeding of dogs and pigeons by human beings 2.) We can see remarkable changes in the fossil record 3.) The selection during the breeding of dogs and pigeons is caused by a teleological agent (i.e., human beings) 4.) Therefore since the results are similar, the selection which resulted in the fossil record is also caused by a teleological agent (i.e., Intelligent Designer = God)

boby said: ..........If, on the other hand, there were no evidence that the object had been manufactured, we could not conclude design. Either we would conclude that it was a natural object (i.e. formed by natural processes) or we would have to conclude that we simply didn't know. exactly and let me use YOUR logic: it there were not evidence that LIFE had been manufacture we could not conclude deisn. Either we would conclude that LIFE was a natural object (i.e. formed by natural processes) or we would have to conclude that we simply didn't know. back to the beginning again: How do YOU determine that an object was made by natural processes???

Tom Marking said: "How would you do this? Please design an experiment (or experiments) that would make this possible for any organism of your choice." What the heck. You guys are the ones claiming you're observing these effects in pigeons, dogs, land snails, etc. You mean you can't quantify your observations of these effects (e.g., natural selection, genetic drift, etc.)? Why does it require a new experiment? This should be routine biological science.

bigbang said: Nigel asks: "BTW, you did not answer my question. How come Behe cannot explain the origin of nylonases?" . Apparently Behe considers it trivial.

When asked if the independent evolution of nylonase in two different strains of flavobacterium and of pseudomonas aeruginosa was a good example of an increase of information in the genome; and whether it refuted the main contention of his book, Behe replied: “No. Those enzymes are very simple ones which simply hydrolyze precursors to nylon. That’s a very simple task, which can be done even by small organic catalysts.”

You know Nigel, Behe’s EoE is now selling for only $7 at Amazon----you should order yourself a copy if for no other reason than to find and expose all the lies and poor scholarship that you and everyone else here is convinced that Behe is guilty of.

Contrary to your POV, I myself find Behe rather interesting, knowledgeable,

likable, a very good writer and explainer of a rather difficult subject,

a rebel of sorts; and I suppose I tend to like people capable of thoughtfully and intelligently bucking consensus.

Seems to me he’s taken a lot of unnecessary abuse from the neo-Darwinan consensus crowd, and yet he’s generally rather calm and civil.

Anywho, since we now realize that the universe isn’t infinite and eternal after all, but rather that it did indeed have a beginning, a beginning with inexplicably low entropy;

and since we now realize how finely tuned things seem to be;

being an atheist is no longer as intellectually satisfying as it once was,

whereas believing in first cause/design is.

So I'm no longer an atheist and the question is how far down the design goes----I suppose that life and we sentient beings might still be an accident, or maybe a product of Dawkins’s space aliens, but I’m not yet convinced.

Tom Marking said: "Natural selection, genetic drift, etc can be observed and it is possible to say that in one situation one of these has been more important than another. However, as far as I know it is not possible to put even approximate figures for the relative importance of each. To begin with, exactly what would you be measuring?" O.K. Let me propose an experiment, but I'm sure many, many biologists have thought of things like this before and probably much better. 1.) Genetic drift group - You put 1,000 Drosophila melanogaster in some type of enclosure which we call the reference environment. It has some standard amount of food and type of food. You let the population evolve. You do sampling every so often (maybe every day you pull out 10 at random and sample their genome). You see how the genome varies with time. This gives you some idea of genetic drift when there is no particular selection pressure being applied. 2.) Natural selection group - 1,000 Drosophila melanogaster in an enclosure of the same size. You slowly vary the type of food from let's say something sucrose-based to some other sugar that's harder to digest. You do the same sampling of the genome. This should give you some idea on how the genome is varying when the population is under stress and therefore undergoing selection. And there could be various natural selection groups where you vary different aspects of the environment such as temperature, amount of food, etc., etc. So that's the type of experiment I would run in order to get some idea on the relative importance of selection versus genetic drift. But I'm sure there are experts who have thought about this and have much better ideas for experiments.

Tom Marking said: "Intentional behavior on the part of some organisms does not imply that evolution of a species (theirs or another) was also intentional on the part of something else." Let's perform a thought experiment, which sadly, is not too different from reality. Let's say Homo sapiens decided to drive into extinction all species of the class amphibians. To a certain extent this is already a real possibility but let's assume it became public policy. Is there any doubt that we couldn't achieve this goal? Now, let's say humans go extinct and some other intelligent species evolves in our place millions of years from now. When that intelligent species' geologists examined the fossil record they would note a sudden dissapearance of the class amphibia in the fossil record. Such an evolutionary signature would be teleological and perhaps the intelligent species of the future would even be able to deduce that it was purposeful. So from their point of view certain aspects of evolutionary history would be teleological and others wouldn't be. It would be a mixture of the two. And all of this would be true even without an Intelligent Designer.

There are three problems I foresee with your experiment: (a) How can you be sure there is no selection pressure on your “control” group? There will obviously be competition for opportunities to reproduce, and thus differential reproductive success according to heritable traits that lend themselves to increased mating.

bigbang said: Anywho, since we now realize that the universe isn’t infinite and eternal after all, but rather that it did indeed have a beginning, a beginning with inexplicably low entropy; and since we now realize how finely tuned things seem to be; being an atheist is no longer as intellectually satisfying as it once was, whereas believing in first cause/design is. So I'm no longer an atheist and the question is how far down the design goes----I suppose that life and we sentient beings might still be an accident, or maybe a product of Dawkins’s space aliens, but I’m not yet convinced.

Tom Marking said: "If species A wipes out species B, then that’s what it was. Evolution doesn’t care about the reason." If that's true then why are we arguing at all? Why did Darwin spend 30 years of his life searching for a mechanism to explain evolution if the mechanism doesn't matter? You could have natural selection, Yahweh mucking around with DNA, the Flying Spaghetti Monster mucking around with DNA, etc., etc. and as long as the result is the same you say it doesn't matter?

Science Avenger said:

Tom Marking said: So you appear to be arguing that the mechanism for the development of a species is important, but the mechanism for the extinction of a species is of no relevance. Great!, I can now go off and claim that natural selection explains the development of each species but it was the Flying Spaghetti Monster that caused all the extinctions.

Sure, if you want. If a species goes extinct, there is no evolution. The whole concept behind selection is that there is nonrandom differential reproduction. A total wiping out of a species doesn't allow for that.

Well sure, but natural selection is still viewed as acting on an organism’s physical characteristics, or phenotype; it’s just that we now know that phenotype is determined by an organism’s genotype and that it’s random mutations to the DNA that provides much of the variation that NS then acts upon.

— bigbang

I must be evolving Larsson b/c I now more or less agree with you—-based on the Evo-Devo discovery that the genes required for building large, complex animal bodies, or phenotypes, were in place millions of years b/f those animal bodies, those phenotypes, even emerged—-that somehow NS was able to select those phenotypes, those traits, obviously products of RM, b/c RM is all there ever was, is, or will be, b/f they even emerged. Now that I think about it, how could it be otherwise?

— bigbang

You say that “fitness isn’t defined by selection but by reproductive success.” Sure, I’ll go with that—-and we know that a trait has reproductive success b/c if it didn’t it would not have been selected: ergo, reproductive success is defined by selection.

So, in conclusion, you claim that NS is a circular argument, but in fact it is a feedback loop.

… since we now realize how finely tuned things seem to be…

Finetuning as a support for a religious anthropic argument is based on a basic misunderstanding of probability.

Larsson says: “We don’t realize that the universe ‘isn’t infinite and eternal’”

.

Well, perhaps you don’t realize it, but, based on the currently available science and evidence, most agree that the universe that we find ourselves in is around 14 billion years old. But of course if that conflicts with your atheistic accidental and/or multiverse world view, then by all means, freedom of religion kind of guy that I am, believe whatever your atheism dictates.

Eric said: Torbjorn (sorry about the missing umlaut), while I don't disagree with you, there is a much simpler response to the fine tuning argument. To whit: any idiot can see that the universe isn’t fine tuned for our type life at all. Consider; the % volume of the universe consisting of earth-like planet surfaces is, what? 0.000000000001%?

bigbang said: Well, perhaps you don’t realize it, but, based on the currently available science and evidence, most agree that the universe that we find ourselves in is around 14 billion years old.

Henry J said:

without explaining the degree of idealization applied, is sometimes perilously close to committing a fraud.

Sometimes?