Scientists, on the other hand, have been exploring other possibilities and testing various models. They have shown that the molecular data is not consistent with sudden origins. Instead it shows that all of the major animal phyla are related and that their common ancestors probably lived millions of years before the Cambrian explosion. Thus, the evidence indicates deep divergence and the lack of transitional fossils does not prove the non-existence of these ancestral forms.
In order to support his creationist view, Meyer has to discredit the molecular evidence. We've already seen that he has five arguments against the data [Darwin's Doubt: The Genes Tell the Story?]. The first three were: (1) there are no transitional fossils [The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes]; (2) different molecular phylogenies do not agree in all detail [Stephen Meyer Says Molecular Evidence Must Be Wrong Because Scientists Disagree About the Exact Dates]; and (3) different genes evolve at different rates [Stephen Meyer Says Molecular Data Must Be Wrong Because Different Genes Evolve at Different Rates].
None of those arguments are correct and one of them (#3) is just plain silly.
His fourth argument is that IDiots are allowed to ignore the molecular evidence because mutation rates are not constant.
Other problems run even deeper, having to do with the assumptions that make comparative analyses possible in the first place. These comparisons assume the accuracy of molecular clocks—that mutation rates of organisms have remained relatively constant throughout geological time. ...Theme
Even if we assume that mutation and natural selection can account for the emergence of novel proteins and body plans, we cannot also assume that the protein molecular clock ticks at a constant rate.
MutationI'm not sure if Stephen Meyer understands what causes the molecular clock. It's a combination of mutation rate and the rate of fixation of nearly neutral alleles by random genetic drift [The Modern Molecular Clock, Random Genetic Drift and Population Size]. Modern population genetics shows us that the overall rate of change should be the same as the mutation rate. Since mutation rates are relatively constant, there will be a stochastic molecular clock.
Meyer quotes from a 1999 paper by Valentine, Jablonski, and Erwin.
Valentine, Jablonski, and Erwin note, "Different genes in different clades evolve at different rates, different parts of genes evolve at different rates and, most importantly, rates within clades have changed over time.This is an accurate quote. Valentine et al. were critical of the exact dating of the splits between various animal phyla although they noted that there was general consensus on deep divergence. They also noted that, regardless of rates, the overall pattern does not suggest rapid radiation. They said,
The new data, primarily from 18S rRNA but more recently from additional molecules, indicate a very different configuration (Fig. 5). Although resolution of the branching pattern within the major groups has been a challenge (though this difficulty is not in itself convincing evidence for a rapid evolutionary burst; see Abouheif et al., 1998), the new basic framework appears robust. Some changes should be expected in the placement of groups within the framework, especially groups wherein relatively few taxa have been sampled.The observation that different genes evolve at different rates and different parts of the same gene evolve at different rates is trivial. I fault Valentine et al. for mixing up several different observations in their 1999 paper and even in the 2013 book by Erwin and Valentine.
Molecular clocks are based on the rate of substitution at neutral sites. Some genes have more neutral sites than others and some parts of genes have more neutral sites than other parts that are more highly conserved. The rate of change is measured as the number of changes at these sites and not the rate of change over all amino acids in the protein.
Valentine et al. also discuss the calibration of the molecular clock—that is the rate of change per year as calibrated against known divergences based on the fossil record. This calibration is difficult but Valentine et al don't distinguish between those calibrated rates and the mutation rates that underlie the molecular clock. In those cases where we have reliable dates (e.g. hominid evolution) we now know that the rates over millions of years are very close to the known mutation rates in extant species [see Mutation].
Valentine et al. do seem to imply that mutation rates are different in different lineages and not just that the calibration of rates can be a problem in some lineages.
I don't believe they are correct. All the evidence we have suggests that the overall mutation rate due to errors in DNA replication are pretty constant in different lineages and, presumably, over time. Thus, our theoretical understanding of molecular evolution suggests that there should be an approximate molecular clock and that's what the data overwhelmingly shows in almost all cases.
But even if I'm wrong it would be an extraordinary coincidence if all the changes in mutation rate just happened to completely obscure the fact the all the modern animal phyla sprang into existence at the same time about 520 million years ago as Stephen Meyer believes.
Meyer also quotes a paper by Ho et al. (2005) where the opening sentence of their introduction says, "The rate of molecular evolution can vary considerably among different organisms, challenging the concept of the 'molecular clock.'" The authors don't offer any evidence to support this statement. The paper is about constructing trees from simulated data where some of the algorithms allowed for rate changes in different lineages. This is not very good support for the idea that mutation rates can vary considerably in different lineages thus invalidating one of the key assumptions of the molecular clock.
Keep in mind too that molecular clocks are calibrated based on the estimated age of presumably ancient fossils. If, however, such estimates are incorrect by even a few million years, of if the fossil used to calibrate the mutation rate does not lie at the actual divergence point on the tree of life, the estimated mutation rate may be badly skewed.Myer is confused about the difference between calculating the actual mutation rate in changes per year and whether the mutation rate is relatively constant over time. We all agree that calibrating the rate of molecular change is difficult—although we are reaching a consensus on values that clearly place the divergence of major animal phyla in the Precambrian. On the other hand, there is widespread consensus that the underlying mutation rates are pretty much the same and that means there IS a molecular clock as predicted by population genetics.
It's true that calibrating the molecular clock is difficult, though not as difficult as Meyer claims. It's not true that the underlying theory is wrong and mutation rates vary considerably from lineage to lineage thus invalidating molecular phylogeny.
Ho, S. Y., Phillips, M. J., Drummond, A. J. & Cooper, A. (2005) Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution 22:1355-1363. [doi: 10.1093/molbev/msi125]
Dunn et al. (2005) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749 [doi: 10.1038/nature06614]
Valentine, J. W., Jablonski, D. & Erwin, D. H. (1999) Fossils, molecules and embryos: new perspectives on the Cambrian explosion. Development 126:851-859. [PDF]
Nice post. I do think one should be careful with phrases like "vary considerably" though: in the tree you gave, the minumum and maximum root-to-tip distances differ by more than a factor of two - I would certainly call this variation "considerable" and take the tree as illustrating just how crude the molecular clock approximation is. This does not affect your point (none of this invalidates molecular phylogeny - in fact, these are _conclusions_ of molecular phylogeny), but naysayers could use it as grounds for disregarding your argument without addressing its substance.
ReplyDeleteI am not sure I understand you correctly. It is well understood in my area that different loci do have very different mutation rates - think chloroplast coding regions, which are damn near constant below the family level versus nrETS which can hardly be aligned across a plant family. Likewise, it is well understood that short-lived species evolve faster than long-lived ones and that parasitic plants often stand out from their relatives by having faster rates of change in the non-coding loci we traditionally like to use for phylogenetics.
ReplyDeleteOf course, none of this means that we cannot trust the analyses because partitioned, relaxed and local clock approaches have been developed to deal with precisely this situation. But this is the situation.
In orchids, some lineages (eg in the Oncidiinae) have much longer branches than others. These are often lineages that have adopted a "twig-epiphyte" lifestyle, specializing in rapid growth and reproduction on a short-lived microhabitat. The long branch lengths for these species compared to their "normal" relatives indicate a faster effective mutation rate per year. I imagine there is a fairly constant mutation rate per unit time, plus a mutation rate per sex cell division. There are more sex cell divisions per year in these species than in normal orchids, because of their very short generation times (maturing in a year or two compared to four to seven or more years in normal orchids). So there are more mutations per year, and much longer branches, in these twig epiphytes than in normal orchids.
ReplyDeleteIf generation times in the Pre-Cambrian were systematically significantly shorter than post-Cambrian generation times (and this might be expected since the Pre-Cambrian organisms would be smaller), I can imagine that the mutation rates per year might have been higher then, causing us to overestimate the pre-Cambrian depth of the divergence.
None of this, of course, supports Meyer's view that the depth is zero. I am just suggesting caution about how much we really know here. And maybe people who know more than me on the subject can correct me if I am wrong.
Lou Jost
I think there is some terminological muddle here. Substitution rates differ from locus to locus. This may or may not reflect differences in mutation rates. When the underlying mutation rates are the same, there can still be different fractions of mutations that are eliminated by purifying selection, so that are different substitution rates resulting.
ReplyDeleteI think that most of the big differences in substitution rates between loci are the latter -- different loci are under different amounts of scrutiny by natural selection. In some almost all mutants are screened out as too disruptive to function. In other loci natural selection is more tolerant.
So I suggest that, however much mutation rates may vary among loci and and among lineages, substitutions per mutation are the main thing that varies.
Also, I point out that molecular phylogenies can be reconstructed without any assumption of a clock, even of a clock within loci.
correction: "... so that different substitution rates result."
DeleteIt seems very likely that a major cause of differences in substitution rates among taxa is difference in mutation rates. I say this because, although substitution rates certainly vary from locus to locus, there are taxa for which the substitution rates at all loci examined are considerably above the general rate. (And I'm referring to my own data here, e.g. Hackett et al. 2008 and Harshman et al. 2008. Tinamous, in particularly, have a uniformly much higher rate of evolution for each of 20 loci than do other paleognaths.) I'm not thinking immediately of another factor that would affect the rate of neutral evolution across the genome. I suppose that population size variation would affect the rate of nearly neutral evolution across the genome, if that's what we're talking about. But this requires that introns, among other things, be evolving nearly neutrally, not neutrally.
DeleteThis has nothing to do with reconstructing phylogenies, though it certainly has something to do with time-calibrating them. Meyer misunderstands both.
You might be right about that, but I hold out for differences in substitutions per mutation when explaining different rates between different loci.
ReplyDeleteThat's probably most of it, at least. I'm talking only about systematic rate differences among taxa.
DeleteDNA doesn't show we are related. it just shows like DNA. it would be this way if a creator built everything. A common blueprint or common physics in genetics.
DeleteThe Dna is silent about origins and processes. Its speculation, right or wrong, that supplys the substance of conclusions.
Its a great point about questioning a DOMINANT assumption of molecular clocks ticking as they do now!
Who says and why say they tick as they always did.
Even if they did it would still be just a line of reasoning.
I don't there is, or could be even if true, scientific genetic evidence that the molecular clocks is static from the start.
ID folks got this right.
'They told me you had been to her,
DeleteAnd mentioned me to him:
She gave me a good character,
But said I could not swim.
He sent them word I had not gone
(We know it to be true):
If she should push the matter on,
What would become of you?
I gave her one, they gave him two,
You gave us three or more;
They all returned from him to you,
Though they were mine before.
If I or she should chance to be
Involved in this affair,
He trusts to you to set them free,
Exactly as we were.
My notion was that you had been
(Before she had this fit)
An obstacle that came between
Him, and ourselves, and it.
Don't let him know she liked them best,
For this must ever be
A secret, kept from all the rest,
Between yourself and me.'
It's about time that Rule Forty-two was invoked.
DeleteIt's about time that Rule Forty-two was invoked.
DeleteI have a towel. I'm pretty sure Joe Felsenstein has a towel.
John, do you have a towel?
I do, but I'm panicking anyway. What is rule 42?
Delete`Rule Forty-two. ALL PERSONS MORE THAN A MILE HIGH TO LEAVE THE COURT.'
Delete(From ALICE'S ADVENTURES IN WONDERLAND, Chapter XII Alice's Evidence)
On the internet, nobody knows if you're a mile high. Anyway, you're nothing but a pack of cards.
DeleteI thought it was some Irish thing about non-Gaelic games not permitted in Gaelic League stadiums.
DeleteAs has been pointed out before, there's something of the Beat poet in Byers' screeds. I'd love to sit in a San Francisco cafe in 1953 and listen to someone read his comments while beating intermittently on a bongo drum.
DeleteSnap your fingers and sip your espresso and we will all groove together:
"Just a Line of Reasoning"
By Robert Byers
Its a great point about questioning
a DOMINANT assumption
of molecular clocks
ticking as they do now!
Who says and why say
they tick as they always did.
Even if they did
it would still be
just a line of reasoning.
I don't there is, or could be even if true,
scientific genetic evidence that the molecular clocks
is static from the start.
ID folks got this right.
Groovy man. Richard Brautigan lives again!
This is off topic, but I started a Twitter account (DiogenesLamp0). I will only tweet you my funniest one-liners.
DeleteRichard Feynman was known to play the bongo drums.
DeleteNow that I would pay to see.
I will never tweet you what I'm eating or drinking, and I've cut down on nude self-portraits almost 50%.
DeleteHowever, we have evidence, strong, to make Larry feel uncomfortable.
DeleteNot at all. There is the evidence, and then there is the way papers are written and presented.
Well, Mr. President, it's the bees and spiders again. They stole my food stamps and sold them to the rats! I went downstairs for to honk the horn for help, but the snakes is guardin' it for the cockaroaches. Oh, Mr. President, I ain't been inside for a week, and I know my wife is sleepin' with the bees!
Deleteok this is all too hilarious.
DeleteI think it was Oberski who first pointed out the beat nature of Robert's discourse. Diogenes lays it out very nicely. Steve's idea of adding Feynman on the bongos is just too much.
Shouldn't we all be dropping acid at this point?
Somewhere in the smokey cavern to the beat and wisdom of Byers the barkeep will become jesus who will tell us when time really started and the answer will probably be yesterday, or not yet.
DNA doesn't show we are related. it just shows like DNA.
DeleteHey booby, if a woman hauls you into court claiming you are the father of her baby, a DNA test, which is accepted everywhere in Canada and the US will prove it one way or the other. Try telling the judge that DNA doesn't prove relationship.
I am still convinced that Bobbie is a sophisticated Poe. I bet he's having loads and loads of fun.
DeleteRobert, please understand something: What I know about genetics and DNA is that we can determine with a very high degree of certainty if a mother/father couple are the parents of their own children - and vice versa.
ReplyDeleteAs a matter for fact, correct determination of family relationship is a matter of making certain that an organ transplant is possible. Without that very precise tool for determining family relationships, organ transplantation would be like playing russian roulette with the patients life - with a fully loaded barrel.
Now please reference any, any evidence, research or reliable source for your claims about DNA and heredity. Unless you can produce supporting evidence for your claim, you should state clearly that you make claims about things you don't know anything about.
Nope, the apparent similarity between the DNA of parents and children is just because the Creator uses similar blueprints for parents and children: "The divine fatherhood is the source of human fatherhood." (Ephesians 3:14)
DeleteIncidentally, ID predicts that similar DNA can also be found between masters and servants: "A son honours his father, and a servant his master." (Malachi 1:6). This prediction has been borne out in many cases, mistakenly interpreted by brainwashed scientists as casting doubt on parentage. Respect the beat poet.
Rolf Aalberg
DeleteYou make my case.
Its not a knowledge of the subject but a criticism of the methodolgy used in the subject. Thats my big point I strive to persuade on.
Its true about Dad/me DNA being evidence of our biological relationship.
Yet other things are also used to back this up. Anyways its still JUST a line of reasoning, however reasonable to someone, that say its DEMANDING that extrapolation backwards leads to conclusions about biological relationships between life forms. Us and apes and bugs etc.
HOWEVER. Its also a line of reasoning to say a creator with a common blueprint or computer program also would have like dna for like biology. So only being a special case about in-kind types and DNA proof of relationship.
people can be connected by DNA but not out of out kind.
I'm saying that even if it was true or what not true, about relationship connections, the genetic assumption of a constant ticking clock of molecular action backwards nulligy's it all as a scientific conclusion.
Your dad/me thing being extrapolated back to when we were fish is just a line of reasoning and not science.
You show me you are persuaded by a line of reasoning and not by scientific genetic evidence.
Scientific methodology error has been the problem in origin issues and NOT researchers failure or the critics failure.
If the question is What is scientific evidence then what is it??
Now imagine if Byer's comment were read in concert by Laurie Anderson.
DeleteWe see a bare, darkened stage blowing with dry ice fog, raked by the beams of purple lasers. Laurie Anderson enters, wearing a black leotard emblazoned with neon lights and glow sticks. She stands before a rear-projection screen showing black and white footage of the collapse of the Tacoma Narrows Bridge and other disasters. Her hair is short and spiky. She tilts her head forty-five degrees and, in a voice simultaneously girlish and machine-like, she declaims:
"Relationship Connections"
By Robert Byers.
Its true about
Dad/me DNA
being evidence of our
biological relationship.
Yet other things are also
used to back this up.
Anyways its still
JUST a line of reasoning,
however reasonable to someone,
that say its DEMANDING
that extrapolation backwards
leads to conclusions
about biological relationships
between life forms.
Us
and apes
and bugs
et cetera.
HOWEVER. Its also
a line of reasoning
to say a creator
with a common blueprint or computer program
also would have
like dna for
like biology.
So only being
a special case about
in-kind types and
DNA proof of
relationship.
people can be connected
by DNA but
not out of out kind.
I'm saying that even
if it was true or
what not true, about
relationship connections,
the genetic assumption
of a constant ticking clock
of molecular action backwards
nulligy's it all
as a scientific conclusion.
Your dad/me thing
being extrapolated back to
when we were fish is
just a line of reasoning
and not science.
You show me you
are persuaded by
a line of reasoning
and not by scientific
genetic evidence.
Scientific methodology error
has been the problem
in origin issues
and NOT researchers failure or
the critics failure.
If the question is
What is scientific evidence
then what is it??
Robert, how can ID folks get anything right when the world is only ~6000 years old?
ReplyDeleteYour only argument WRT evolution should be: Since the world is only ~6000 years old, all scientific biology is nonsense. Please confirm.
Rolbert, a statement like "people can be connected by DNA but not out of out kind." makes no sense.
ReplyDeleteAll humans share a common set of genes, DNA. No species, not even chimpanzees share the same DNA. But here's the catch. All chimpanzees also share a common genome - a genome distinct from that of any other species as well.
That's why we have species: They are genetically separate from all other species - but also more or less related to other species.
The same pattern that we find between the genes of different individuals within a species is also found between the genes of different species.
Like individuals may be close or more remote from each other genetically, species are also more or less closely related genetically.
And here's something for you to ponder (preferably, to study, because you only try to reason answers to your problems, but like you cant squeeze apple juice out of oranges, you can't squeeze facts out of a brain where such facts are absent. It is like a carpenter should lecture an attorney on law.)
So what you shuold ponder - after having obtained the required knowledge, is the fatc that there is a family tree between all species just as there is a family tree between all humans.
And the molcular clock isn't something you need bother about - it is just a tool to faciliate determination of timing of genetic events. It makes more accurate dating of past events possible. The theory of evolution was thriving before the advent of molecular clocks and would thrive happily along even if it could be show that molecular clocks are useless.
Study, Robert, try to learn something before you talk. You might enjoy learning why humans have to suffer hiccups; the reason is a fish gene. What would a fish gene do in a human body?
Again you use the commonness of DNA to demand it equals descent. Even if true your just trying to persuade me based on a line of reasoning. NO scientific evidence is provided to back up your assertion.
DeleteSo ALL i need to do is suggest another option for why DNA could be same for unrelated biological agents.
simply a common programme or blueprint underlying all biology.
Just like in physics. this is what I would do if I created things.
Like livers equals like DNA score for like livers.
Yet it doesn't mean one can use DNA to say all livers come from a original type of liver in a early fishy bug etc back in the day,.
I stress again about methodology.
It need only be and could only be that like bodies equals like DNA from a simple single law in biology.
My having chimp DNA is not SCiENTIFIC EVIDENCE i'm related to a chimp. Its just a logical deduction based on a assumption.
So my point stands that no scientific evidence is provided for these extrapolations backwards using molecular clocks or and genetic stuff.
All you guys are telling us is that its UNREASONABLE to reject species DNA points as proving genus/family relatedness.
I say gOd would do that anyways.
Nevertheless the point is once again about scientific genetic evidence.
I don't see it because you don't have it to show us.
I don't see where my logic is wrong on this.
You are completely ignoring the history of the field.
DeleteCreationists like to talk about how evolution is not a testable theory. Which is completely false and similarity in DNA is a great example,
DNA was only shown to be the carrier of heredity in the 1940s, the structure was determined in 1953, the genetic code was worked out by the 1960s, and DNA sequencing only became routine by the 1980s.
That's more than a 100 years in which phylogeny was entirely based on comparative morphology, anatomy, embryology, etc.
The prediction was that molecular phylogeny will mostly match what has been learned through those methods.
And it indeed did.
A lot of relationships were revised but pretty much none of them were of the kind that would have invalidated common descent. The Articulata hypothesis might have been rejected, but humans are still closest relatives to apes.
It's very convenient to claim that molecular phylogeny represents circular reasoning if you're a creationist, but that's just a typical case of creationist ignorance
@Georgi,
DeleteI don't mean to be picky but the first molecular phylogenies were published in the early 1960s'. That's twenty years before you say that DNA sequencing became common. See: The Modern Molecular Clock.
That doesn't change your main point, which is that IDiots tend to be, well, idiots.
Thanks for correcting that.
DeleteI was really thinking about DNA sequencing itself though, thus the error
As long as we're picking nits, here are the customary, obligatory ones: 1) it's not the similarity so much as the nested hierarchy that shows common descent and 2) humans are just closest relatives of apes, we are apes.
DeleteYou do mention the correspondence among trees from different data sets, which is an indirect way of referring to nested hierarchy, but it isn't just between molecules and morphology; it's also consistency within data sets, e.g. high bootstraps, significant likelihood ratio differences, etc. And of course our closest relatives aren't just apes, they're chimpanzees, and we are nested within apes.
...not just closest relatives...
DeleteAnd of course our closest relatives aren't just apes, they're chimpanzees, and we are nested within apes.
DeleteI am fully aware, I did not phrase it correctly
But the best is that phylogenies built with, for example, DNA stretches whose particular sequence does not matter, give us the same relationships. This is also true of viral insertions, SINEs, LINEs, etc. So it's not only the parts that have some work to do, and therefore some relationship with the phenotype. Less phenotypically compromised data agree.
DeleteYes, that's very good point too and I was thinking of making it. However. you know how they're going to come back to you - "Well, junk isn't junk and will be eventually found to be functional"///
DeleteMeyer says: "Other problems run even deeper, having to do with the assumptions that make comparative analyses possible in the first place. These comparisons assume the accuracy of molecular clocks— "
ReplyDeleteComparative analyses do not use a molecular clock nowadays. Perhaps one method did so 30 years ago, but those days are long past.
Meyer shows he has not taken the trouble to look at the methods actually used.
So Larry,
ReplyDeleteIt’s been almost 3 years since I asked you, “can you cite experimental data that demonstrates that irreducibly complex structures can arise by purely natural causes?” You never answered my question, you simply ignored it. I’ve since searched and searched for any indication that experimental research has produced an irreducibly complex structure by natural causes, but just can’t seem to find any.
All I can find are mostly personal blogs of Darwinists containing musings on how it might be possible like yours containing irrefutably “scientific” statements like: “one can quite easily construct plausible scenarios where each step in constructing an irreducibly complex system confers a selective advantage. All you have to do is postulate that the intermediate selective advantages are not the same as the final purpose of the system.”
So how ‘bout it? Can you please put your money where your "scientific" mouth is and point me to a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely naturalistic causes?
Why does each step have to confer selective advantage?
DeleteJcc queries: "Can you please put your money where your "scientific" mouth is and point me to a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely naturalistic causes?"
DeleteNatural arches and we're done.
And now it's our turn.
Can you please put your money where your "religious" mouth is and point me to a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely supernaturalistic causes? To be more specific, as caused by an invisible, intangible spook or spirit of any type or class.
Prepare for the goal post shifting!
As anticipated, Larry is nowhere to be found. I asked a perfectly valid question and he lets one of his lackeys give a perfectly vapid response:
DeleteNatural arches and we're done.
How silly. Exactly what biological function an erosional remnant performs, God only knows. I should have known that Behe’s definition of “being composed of several well-matched, interacting parts that contribute to the basic function” is obviously irrelevant and superfluous to my original question…
jcc,
DeleteHow about the Krebs cycle? I'm not sure if you read this before or not, but I personally found it interesting. Niall Shanks and Karl Joplin discussed a couple examples of complex biological systems arising via natural processes in this paper, and the Krebs cycle is one of them:
Redundant Complexity: A Critical Analysis of Intelligent Design in Biochemistry
I think that the examples that they discussed amply demonstrate that it is not only possible for complex biological systems to arise via natural processes, but in fact they do, and you can do the experiment yourself in a lab.
ShadiZ1:
DeleteHow about the Krebs cycle?
Yes, how about the Krebs cycle? I’m no expert, but it doesn’t take a rocket scientist to see the glaring causal circularity (another form of irreducible complexity) that it’s embedded in. This animation describes the Krebs cycle, but please note the initial conditions: the cycle begins with glycolysis—a reaction that
requires the presence of ATP. The Krebs cycle takes place within the mitochondrion—which produces…ATP. Dare I say, removing the ATP from the initial conditions results in no glycolysis which results in no Krebs cycle in the mitochondrion. A classic chicken and egg conundrum.
Like I said, I’m no expert so I’ll just defer to the response to Shanks & Joplin’s paper by the man who started the whole IC “controversy,” here. And, another great response to this whole subject can be found here.
Thanks.
@ShadiZ1
DeleteUnfortunately, the paper by Shanks and Joplin that you linked to is embarrassing. Their defense of the citric acid cycle (Krebs cycle) bears no relationship to how it actually evolved. See A Torley Defense of Irreducible Complexity.
Michael Behe did a fine job refuting Shanks and Joplin in the paper that "jcc" linked to.
The rest of the article by Shanks and Joplin is just as embarrassing. Their explanation of the evolution of the glycolysis pathway reveals a profound misunderstanding of biochemistry and evolution.
However, in spite of the fact that the explanation was incorrect, "jcc" responds with a typical IDiot counter-argument. No matter how well you can explain the evolution of an irreducibly complex system, the IDiots will always pick out one of the original components and challenge you to "explain that!" In this case it's ATP.
It's like trying to nail Jello to a wall. It always oozes down to the floor.
Not only that, like most IDiots "jcc" doesn't have a clue what he's talking about. ("I'm no expert, but it doesn't take a rocket scientist ...") Actually, it DOES take a rocket scientist (i.e. expert) to explain the evolution of biochemical pathways. They would know that the initial reactant (acetyl-CoA) can come from many sources, especially fatty acid oxidation. Fatty acid oxidation does not require ATP—neither does glycolysis for that matter.
Experts would also know that the citric acid cycle evolved more than a billion years before mitochondria.
jcc asks,
DeleteSo how ‘bout it? Can you please put your money where your "scientific" mouth is and point me to a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely naturalistic causes?
You are moving the goalposts. IDiots argue that the evolution of irreducibly complex systems is IMPOSSIBLE. Thus, God must have created them.
In order to refute that argument, it's only necessary to show one plausible example of the evolution of an irreducibly complex system. I picked the citric acid cycle, which is clearly an irreducibly complex system, and wrote up an evolutionary explanation that I published in my textbook.
The evidence that I describe is the existence of species that do not have a citric acid cycle but still have all the enzyme but one. The missing enzyme needed to complete the cycle is α-ketoglutarate dehydrogenease and that enzyme is clearly related to another enzyme (pyruvate dehydrogenase) that catalyzes a very similar reaction.
Only an idiot would deny that this explanation is impossible.
Only an idiot would deny that this explanation is impossible.
DeleteYou should probably fix that.
Right. It should be "Only an IDiot would deny that this explanation is POSSIBLE. Thanks.
DeleteDon't you wish we could edit comments?
Listen up punks. All of you should pay attention to this exchange, because in debating the IDiots we have to anticipate the ten million ways that they equivocate and play word games. So pay attention.
DeleteNote that JCC above shifted the goalposts-- exactly as I predicted. He asked a question which he presented as un-answerable; I answered his question accurately. He responded with name-calling, goalpost shifting, and genetic fallacy. Do IDiots have any evidence for their position or is it all name-calling and equivocation? As we'll see, no.
Textbook example of equivocation: JCC's original comment said nothing about function of any kind, "biological" or otherwise. When I answered his question, he shifted the goalpost to "biological function", which was NOT mentioned in his original comment and is NOT a part of Behe's definition of irreducible complexity!
Behe's definition of IC is NOT limited to biological function, nor would it make any sense if it were, because Behe is drawing an analogy between biology and MACHINES. Behe is constantly blathering about mousetraps, bicycles, and Rube Goldberg machines, and sometimes artworks, none of which serve a biological function. Thus IC is not and cannot be limited to "biological function", but above IDiot JCC inserted it in an ad hoc fashion-- the ten millionth time that an IDiot has employed equivocation to evade falsification.
Behe's hypothesis is that natural processes cannot produce an IC system. His hypothesis is presented as falsifiable. But, when falsification is demonstrated (which it has been, again and again and again, inside and outside biology) all IDiots respond by changing the the definitions of almost every word in Behe's definition-- "several", "part", "basic", "function", "remove", etc. to evade falsification.
In the above exchange, the meaning of "function" is equivocated by JCC-- even though Behe's definition says "basic function" (he does not define "basic", natch, Behe needs deniability), not "biological" function. IDiot JCC seeks to evade falsification by re-defining Behe's "function" on the fly. Why do you think that is?
Continued below:
Each word in the definition of IC by itself has at least two or more definitions employed by IDiots, and the IDiots switch back and forth between them. Here's how the trick works:
DeleteThere is no one, single definition of Behe's Irreducible Complexity nor of Dembski's Specified Complexity which SIMULTANEOULSLY has these three properties, ALL of which are logically essential to infer supernatural intelligent causation:
1. Property is observed in biological structures.
2. Never observed to be produced by natural processes.
3. Observed to be produced by immaterial, invisible and intangible spirits.
No ONE definition of IC nor of Dembski's Specified Complexity has all three (3) properties simultaneously, the IDiots create that illusion by equivocating between definitions of every single word they use.
In the specific case of IC: for all the words in Behe's definition-- "several", "part", "basic", "function", "remove"-- there must be broad definition and a narrow definition.
A. The broad definition (e.g. several = 2 or more, part = protein or complex of proteins, function = original function, remove = imagined in thought experiment, etc.) is used to claim that IC systems have been observed in biology (property 1, above).
B. The narrow definition (e.g. several = more than 3, part = amino acid or smaller, function = any function, remove = deleted in genetic knockout mouse, etc.) is used to claim that no IC system can be produced by evolution or any natural process (property 2, above).
I hope that you, the reader, have noticed that the "broad" definition of IC has property 1 but not 2 (it's observed to be produced by natural processes); while the "narrow" definition of IC has property 2 but not 1 (it's never observed in biology, thus irrelevant to evolution).
To sum up: we know that "broad" IC is produced by natural processes; and we know that "narrow" IC is irrelevant to biology.
The specific falsifying example that I gave was of Natural Arches, aka Natural Bridges. IDiot JCC seeks to evade falsification by ALTERING Behe's definition of IC by limiting "function" to "biological function." I explained above why and how IDiots cheat.
Natural Bridges may not have biological function-- but then Behe's beloved mousetraps, bicycles, artworks, flower arrangements, and Rube Goldberg machines don't have biological function, either.
But it is indisputable that Natural Bridges have function.
From the Wikipedia article I already linked to: In a few places in the world, natural arches are truly natural bridges because there are roads or railroads running across them.
In Virginia, US Route 11 traverses the famous Natural Bridge.
Two additional such arches are found in Kentucky. One, a cave erosion arch made of limestone, is located in Carter Caves State Park and it has a paved road on top. Another, a weather-eroded sandstone arch with a dirt road on top is located on the edge of Natural Bridge State Resort Park in Kentucky. It is called White's Branch Arch (also known as the Narrows) and the road going over it is usually referred to as the Narrows Road.
Another is found in Ponoarele Village, in Romania. It is 60 m long, 13 m wide, features a stone arch 4 m thick, 20 m high, with a 9 m span. It is called God's Bridge (Podul lui Dumnezeu) and it is effectively used for traffic.
The railroad from Lima, Peru crosses the Rio Yauli on a natural bridge near kilometer 214.2 as it approaches the city of La Oroya, Peru.
Irreducible Complexity died with Behe lying and perjuring himself on the witness stand at Dover.
Gonna call me some more names, JCC?
On the topic of Irreducible Complexity, note I recently told Casey Luskin directly to his (internet) face that Behe lied on the witness stand at Dover, regarding what Behe had written on the topic of IC of the blood clotting cascade. Behe's lies were a direct result of the ID habit of equivocating to evade falsification, as I discussed above. I presented numerous quotes from Behe's book to prove my point. Luskin tried, but could not defend Behe's lies. As of today he has not responded and really, cannot respond.
DeleteIf you would like to read this exchange on blood clotting, go to American Spectator and start reading at my comment of 9.20.13 @ 10:48PM.
That problems with Behe's misrepresentations on blood clotting which I discuss in that exchange come from my own reading in Darwin's Black Box and on Nick Matzke's devastating takedown of Behe and Luskin, "God of the Gaps…in your own knowledge" at PT, January 4, 2009. A simpler version of the take-down was written by Ken Miller at Carl Zimmer's blog.
JCC, if you know Casey Luskin or any fellow of the DI, tell Luskin not to respond to me at American Spectator. Tell him that if he wants to respond, then open comments at ENV, or respond at my blog, or else I will debate Luskin or any or all of the senior fellows of the DI, alone or in combination, in a face-to-face debate.
Larry,
ReplyDeleteMichael Behe did a fine job refuting Shanks and Joplin
Please explain how an “idiot” could possibly do such a thing? I suppose we’re to conclude that Shanks and Joplin are even bigger idiots than Behe, in your considered opinion?
No matter how well you can explain the evolution of an irreducibly complex system, the Idiots…
I just love assertions like these. Predictably, you inevitably fall back to your pompous argument from authority tactic. Tell me, exactly how many occurrences of irreducibly complex systems have you actually observed evolve?
And then there’s the obligatory:
Not only that, like most IDiots "jcc" doesn't have a clue what he's talking about.
Thus spoke the god of all knowledge. Curious how such a god continues to find it necessary to resort to ad hominem to make his point. I wonder why that is… I also wonder how an “evolutionary” biochemist (though I’m only guessing that his two degrees are actually related to the disciplines of biology and chemistry since I couldn’t find any documentation of what they’re actually in) has convinced himself that possessing those two pieces of paper somehow gives him indisputable authority to judge who is and who isn’t a “scientist.”
Actually, it DOES take a rocket scientist (i.e. expert) to explain the evolution of biochemical pathways.
Yes, you should know, given the countless occurrences of such events that you’ve actually witnessed.
Fatty acid oxidation does not require ATP—neither does glycolysis for that matter.
But that doesn’t negate the fact that ATP is required for how glycolysis currently takes place in the cell. Just because it could occur in a different fashion doesn't prove that it ever did.
You are moving the goalposts.
No, I’m not. You’re avoiding the question. You asked, “Can you cite the articles where they concede that irreducibly complex structures can arise by purely natural causes?” to which I replied: “No, can you cite experimental data that demonstrates that they can?”—the question I repeated above, and the same question you have yet to answer.
A condition sadly corroborated by:
Only an idiot would deny that this explanation is [im]possible.
You’re “moving the goal posts” by refusing to answer the question. As predicted, you only dance around it by “postulating” what’s possible.
Notice that JCC has no reply to my demolition of Behe and of Irreducible Complexity in general, above.
DeleteJCC's hypocrisy is quite perfect, asserting: "Thus spoke the god of all knowledge. Curious how such a god continues to find it necessary to resort to ad hominem to make his point."
DeleteAd hominems? You mean like when you wrote: " I asked a perfectly valid question and he lets one of his lackeys give a perfectly vapid response"
No, you hypocrite, you started with the ad hominems as all IDiots always do.
You use ad homienems and you call my answer "vapid" because you have no response, none, to my total demolition of Michael Behe and Irreducible Complexity, above. Even in principle, IC is dead. Behe lied on the witness stand at Dover. IC is dead.
If it's so "vapid" then you should be able to respond. Over at American Spectator, Casey Luskin had no come-back, and all you've got is name-calling.
Now I'm going to ask once again the question you evaded above: point me to a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely supernaturalistic causes?
To make it extra easy on you, I'll consider as an acceptable response any functional biological system observed to be caused by an immaterial, invisible spook, spectre or ectoplasmic entity of any type or class, including full torso vaporous apparition, non-terminating repeating phantasm, and even a Class Five full roaming vapor.
I got one more question for you, JCC: Does Michael Behe, himself, assert that metabolic cycles are Irreducibly Complex? Including the Krebs cycle, specifically.
DeleteAfter all, you're portraying yourself as knowing what the definition of IC is.
Do you know if William Dembski considers metabolic pathways IC or not?
Do you know if Casey Luskin considers metabolic pathways IC or not?
Do you know if Ann Gauger considers metabolic pathways IC or not?
If you answer wrong, then you're an expert on the definition of IC, are you?
Here's a hint, you science god: calling people names is not an answer to the question.
A biological cell is a natural entity, it is made of atoms, which bind together into molecules and ionic compounds of various sorts. All these entities are governed by the laws of physics through the four fundamental forces, electromagnetism, gravity and the weak and strong nuclear force. The function of the cell is understood through the interactions of all it's constituents through these four fundamental forces. The cell is therefore fully explained as a natural entity, there is no "ghost in the machine" as far as the last 100 years of science has been able to elucidate.
DeleteConsequently, every time a cell divides and replicates itself, an irreducibly complex system with trillions of interacting parts, is arising through purely natural means.
QED.
The cell is therefore fully explained as a natural entity
DeleteReally? Please cite in general, the full scientific explanation of exactly how the first cell arose naturalistically, and specifically, how the specified, complex information in DNA defied the probabilistic resources of the universe and first self-assembled.
There need not have been a first cell.
DeleteAlso, while we're on the subject of inexplicable first things, last time I checked nobody had found a way to reconcile literal Adam & Eve with what we know about human genetics... I am curious to hear if you have a solution to that problem, one would think you do if you are going around demanding various things from people
Georgi and Mikkel, how could you let yourself get sucked into the TARDIS gambit? By TARDIS gambit I mean the tendency of IDiots, when they're caught dead to rights spouting falsehoods, jumping in their time machine and going back a few hundred million years...
DeleteThe IDiot shifted his goal posts. They all do; you have to prepare for that. You, Georgi and Mikkel, instead of hammering his goal posts back where they were originally, you let him suck you back to abiogenesis, which takes us out of biology altogether. This IDiot just shifted the topic of discussion four billion years backward in time and out of the discipline of biology altogether, back to the realm of dead matter, which ain't biology, and is not a problem for biological evolution.
Georgi brings up Adam and Eve? If our IDiot is an Old Earth creationist, he'll have a way of evading that.
He equivocated. He shifted goal posts. Don't change the subject until you get him to address that. It's Gish Gallop.
Georgi Marinov:
DeleteThere need not have been a first cell.
Please explain how that would work.
last time I checked nobody had found a way to reconcile literal Adam & Eve with what we know about human genetics... I am curious to hear if you have a solution to that problem
Can you explicitly state what that problem is?
So since you're not even aware of this problem, jcc, I guess we can safely assume you don't have an answer to it, yes?
Deletejcc writes: The cell is therefore fully explained as a natural entity
DeleteReally? Please cite in general, the full scientific explanation of exactly how the first cell arose naturalistically, and specifically, how the specified, complex information in DNA defied the probabilistic resources of the universe and first self-assembled.
Your challenge was met, and so now you have completely changed the subject. Instead of wanting just one example of how a natural processes give rise to an irreducibly complex system (which you have to concede a single cell diving into two basically is), you want the origin of life explained.
But really, is that what ID amounts to these days, an argument from ignorance? We don't yet know how life originated - therefore design? Brilliant!
Diogenes,
ReplyDeleteyou have no response, none, to my total demolition of Michael Behe and Irreducible Complexity, above.
You mistake my reticence to respond with the wisdom of knowing which conversation is worth my while. Without exception, every time I’ve interacted with an atheist who eventually twists his arm out of its socket patting himself on the back over what a great job he did “demolishing” his opponent, ends up being an exercise in futility for me.
But as a gesture of cordiality and to give you some sense of resolution, I’ll make this exception and reply.
You presented natural bridges as an example of naturally arising, irreducibly complex structures. You also insist that Behe’s analogy includes a reference to machines.
Dictionary.com’s definition of machine is “an apparatus consisting of interrelated parts with separate functions, used in the performance of some kind of work”
Unfortunately, your analogy begs the questions, “what larger apparatuses are these bridges a part of? What specific function(s) do they (the bridges) perform within those apparatuses? And, with the removal of these bridges, what existing function of the larger apparatus will be lost?
Hard questions for an even harder to image irreducibly complex structure…
I hope you are all watching, because you can't debate IDiots unless you learn to deconstruct their texts. Once again, JCC has shifted the goal posts some more, introducing the third, yeah third, definition of "function" in order to evade the falsification of IC.
DeleteTo recap: in JCC's original comment he asked a question which made no mention of "function", certainly not "biological function." His question assumed Behe's hypothesis that IC systems cannot be produced by natural processes, which I quickly falsified by pointing out that natural bridges are IC.
JCC responds with his first equivocation. He now demands "biological function", citing as his authority Behe-- except Behe's definition of IC did not and cannot include "biological function", because Behe's argument is based on an analogy between biological structures and machines-- machines like mousetraps, bicycles, Rube Goldberg machines-- although Behe also throws in random kinds of other shit, like flower arrangements, artworks, Mount Rushmore, or whatever's on the History Channel this afternoon. But the analogy precludes putting "biological function" in the definition of IC. Behe's definition in "Darwin's Black Box" actually said "basic function" but it never defined what "basic function" means, and of course various IDiot authorities keep switching from one definition to another. ID is a clusterfuck of equivocation.
I point this out, so now JCC tries yet another equivocation. Now he pulls something out of his ass that doesn't appear anywhere in "Darwin's Black Box": a brand new, ad hoc requirement, that function (which still isn't defined) must be part of a "larger apparatus".
"Unfortunately, your analogy begs the questions, “what larger apparatuses are these bridges a part of? What specific function(s) do they (the bridges) perform within those apparatuses? "
Ugh what a mess. Behe's definition did not and cannot include "a larger apparatus." The term isn't in any of his definitions of IC (he has about a dozen and I know them all) and the brand new, ad hoc, "larger apparatus" rule is not and CANNOT be part of the definition of IC, because IC relies on an analogy between biological systems and mousetraps, bicycles, etc.
Behe's endless senile blathering about mousetraps never mentioned that they were part of a "larger apparatus." His doddering tedious arglebargle about Rube Goldberg machines never mentioned that they were part of a "larger apparatus." They can't be, because IC is based on an analogy. But Behe endlessly, endlessly repeated that they were indeed IC.
I'll also point out that you're using the phrase "begs the question" incorrectly.
JCC just pulled "a larger apparatus" out of his ass, like the episode of South Park where an alien probe pops out of Cartman's behind.
Why is equivocation mandatory for all IDiots?
I repeat: there is no one, single definition of Behe's Irreducible Complexity nor of Dembski's Specified Complexity which SIMULTANEOULSLY has these three properties, ALL of which are logically essential to infer supernatural intelligent causation:
1. Property is observed in biological structures.
2. Never observed to be produced by natural processes.
3. Observed to be produced by immaterial, invisible and intangible spirits.
No ONE definition of IC nor of Dembski's Specified Complexity has all three (3) properties simultaneously, the IDiots create that illusion by equivocating between definitions of every single word they use.
JCC: Here's a question you totally dodged. Three strikes rule is in effect. We ask a question three times, the third time you don't answer, you concede.
DeleteYou're at two strikes on this one: describe a peer-reviewed publication of an experimentally verified (and repeated) example of an irreducibly complex structure that has arisen via purely supernatural causes.
To make it extra easy on you, I'll take as an acceptable response any functional biological system observed to be caused by an immaterial, invisible spook, spectre or ectoplasmic entity of any type, including full torso vaporous apparition, non-terminating repeating phantasm, and even a Class Five full roaming vapor; also Casper.
JCC: Three strikes rule is in effect.
DeleteYou have one strike on this one:
Does Michael Behe, himself, claim that metabolic cycles are Irreducibly Complex? Including the Krebs cycle, specifically.
After all, you're portraying yourself as knowing what the definition of IC is.
Does ID authority William Dembski consider metabolic pathways IC or not?
Does ID authority Casey Luskin consider metabolic pathways IC or not?
Does ID authority Ann Gauger consider metabolic pathways IC or not?
Do they agree with each other? If not, who's wrong, and why?
I know the answers to those questions; so:
If you don't answer at all, you'll look like an arrogant poser, because, above, you implied you knew more about the definition of Irreducible Complexity than I do.
If you give an incorrect answer, you'll look like a creationist fool, shown up by evolutionists.
If you give the correct answer, Irreducible Complexity is dead... (er).
Regardless, jcc has lost the challenge. When a cell divides, an entire irreducibly complex system is created through a natural process, because all the cellular mechanisms of division and growth are governed by natural processes.
DeleteSo, he's now changed his challenge and moved the goalposts, he now wants to know how the first cell arose. We don't know that, yet. It's a point of ignorance and we're trying to find out.
Will jcc come out and declare that's where his god hides? In current scientific ignorance? IDcreationism always amounts to gap-theology. Where knowledge is uncertain or we don't yet know, well THAT'S where the designer is operating.
How many times in human history have the workings of the gods been supplanted by scientific knowledge? Let's try to list them:
Weather phenomena: Rain, drought, storms, thunder, lightning, hurricanes, tornadoes etc. etc. - all used to be the works of the gods, now we understand it's just physics.
Diseases and disabilites in their thousands. Used to be the works of demons, devils and evil spirits. Punishments by the gods because of all sorts if silly sins like not obeying the sabbath, not sacrificing enough goats, pigs and fruit. Thousands upon thousands of different ailments now explained as due to developmental disorders and infectous microoganisms.
The stars, what are they? The sun and the moon? What are they, where did they come from? Earthquakes, solar eclipses, erupting volcanoes? Used to be the works of the gods. The sun itself was a god for most off human existence. Today, all of it is understood as just more physics and natural processes.
I could go on but I think we get the point. The arena of the gods keep shrinking, where the gods used to control the weather and the celestial mechanics of the heavens, today they're apparently relegated to showing their face on toast or hiding somewhere in the deep geological past where we don't yet know some particular detail about how cellular life arose.
And here we are, proponents of ignorance who didn't get the picture and who don't learn from history are here to tell us that, no.. NO, the gods are still working all around us, just in places we can't see or haven't yet looked. Pathetic.
Rumraket wrote:
DeleteThe cell is therefore fully explained as a natural entity
to which I asked,
Really? Please cite … the full scientific explanation of exactly how the first cell arose naturalistically...
to which Rumraket dodged:
Your challenge was met, and so now you have completely changed the subject.
Yes, he actually accused me of changing the subject. The only explanation I can offer for such irrationality is perhaps the evolutionary path his consciousness and sense of reason took clearly diverged from the primary breeding population long ago, but I digress.
Let me get this straight. Rumraket asserts as fact that the cell is fully explained—but with the exception of its origin. Um, yeah. That’s a, ahem, “full” explanation, all right…how convenient. And according to him, ID is the “argument from ignorance.”
Yep. There’s no “Darwin of the gaps” there. Un-uh.
And then he closes with this swipe:
We don't yet know how life originated - therefore design? Brilliant!
How sad to have convinced himself that he actually lives in a world where rational beings are completely unable to scientifically detect an intentional design when they encounter one…
The first cell is not an extant cell, we understand perfectly well how the cells of today come about. They're natural entities and come about through physics. That's it, game over. Your first challenge was to ask how natural processes give rise to irreducibly complex systems, those challenges were met.
DeleteHere are your exact words: It’s been almost 3 years since I asked you, “can you cite experimental data that demonstrates that irreducibly complex structures can arise by purely natural causes?” You never answered my question, you simply ignored it. I’ve since searched and searched for any indication that experimental research has produced an irreducibly complex structure by natural causes, but just can’t seem to find any.
Now you have. Every time a cell divides this happens. Purely natural causes give rise to an irreducibly complex system.
All you keep coming back to now is to change your challenge to now explaining the origin of the first cell. Looking at the history of science lends zero credibility to a supernatural origin of life, but I see that you've conveniently ignored that and just skipped to asserting what you're trying to prove. It is no mystery why ID is relegated to the margins and forwarded only by religious nuts.
Stay in the bronzeage, jcc.
Rumraket,
DeleteThe first cell is not an extant cell, we understand perfectly well how the cells of today come about.
Congratulations! With that single sentence you not only moved the goalposts, you switched games and moved the stadium, city and country to your intellectually cloistered backyard.
Absurdly claiming as fact that
The cell is therefore fully explained as a natural entity
logically requires a full accounting for its genesis, otherwise it isn’t “fully” explained. Your assertion is tantamount to claiming that the existence of a Saturn V rocket on the launch pad can be fully explained merely by understanding how it achieves everything that it’s observed to do—that is, with the minor exception of acknowledging how it came to be, i.e. it’s blueprints, and the people who built it.
And never mind the irrefutable fact that humans have by no means the slightest clue about so much of what really goes on at the cellular level (e.g. epigenomics).
They're natural entities and come about through physics. That's it, game over.
Really? But if cells are fully understood, then why haven’t geniuses like Larry Boy figured out a way to create them entirely from scratch in the lab? We can create miniature tornados, why not an entirely new species of life?
All you keep coming back to now is to change your challenge to now explaining the origin of the first cell.
No. My original challenge still stands, and your ludicrous attempt at moving the goal posts by claiming that everything is known about a cell, combined with your grossly unscientific assertion that knowledge of extant cells cannot be grounds for hypothesizing about the abiogenesis of the first cell is pure sophistry.
Looking at the history of science lends zero credibility to a supernatural origin of life
Only to anyone who’s either never created anything or has absolutely zero knowledge of engineering systems. But to anyone who does, the universe in general, and life in particular SCREAMS of design. Alas, but I see that you've conveniently ignored that and just skipped to asserting what you're trying to prove. It is no mystery why Darwinism is [rapidly being] relegated to the margins and forwarded only by religious atheist, nuts.
And you keep on keeping your head in the sand, Rumraket.
Rumraket,
DeleteThe first cell is not an extant cell, we understand perfectly well how the cells of today come about.
Congratulations! With that single sentence you not only moved the goalposts, you switched games and moved the stadium, city and country to your intellectually cloistered backyard.
Hahaha, keep up the desperate damage control. We see irreducibly complex systems arising constantly through physics alone. That's nature doing it's thing.
Absurdly claiming as fact that
The cell is therefore fully explained as a natural entity
logically requires a full accounting for its genesis, otherwise it isn’t “fully” explained.
I did, it's just physics. There are four fundamental forces of physics, they are constantly in effect between the basic subatomic constituents of the cell. Whatever the cell does, it does because of the properties of it's constituents. That's how nature and the material world works, of which the cell is a part. Get over it.
Your assertion is tantamount to claiming that the existence of a Saturn V rocket on the launch pad can be fully explained merely by understanding how it achieves everything that it’s observed to do—that is, with the minor exception of acknowledging how it came to be, i.e. it’s blueprints, and the people who built it.
Nope, I told you how a cell comes about through natural means. A cell is irreducibly complex, so your challenge was answered.
Keep up this nervous, feeble damage-control. Keep telling yourself it's not patently obvious what's going on in your head here.
And never mind the irrefutable fact that humans have by no means the slightest clue about so much of what really goes on at the cellular level (e.g. epigenomics).
DeleteWe know to an extremely high degree of certainty that it's just physics. There has never been any observation of a suspension or violation of the laws of physics during cell division and growth.
You're most welcome to demonstrate that physics is not in operation when cells divide. The Nobel Prize awaits!
Really? But if cells are fully understood, then why haven’t geniuses like Larry Boy figured out a way to create them entirely from scratch in the lab? We can create miniature tornados, why not an entirely new species of life?
What a supremely stupid question. Understanding how something works is not a guarantee that you have the technology to physically manipulate structures at those tiny scales. We need to develop the technology first. You could explain how a car is assembled in a factory to some guy living in a jungle with stoneage technology, but just because he now knows how cars are built doesn't mean he can do it himself without the aid of factory machinery. He'd need to get the tools first. We also understand how the night/day cycle happens, it doesn't mean we have the means to rotate the planet.
No. My original challenge still stands
Keep telling yourself this. Yell it out loud if you have to.
I had some formatting issues when I pasted my response so had to redo it a couple of times, here's the last bit:
Deleteand your ludicrous attempt at moving the goal posts by claiming that everything is known about a cell
We know what we need to know to meet your challenge. It's physics, operating on atoms and molecules.
combined with your grossly unscientific assertion that knowledge of extant cells cannot be grounds for hypothesizing about the abiogenesis of the first cell is pure sophistry.
Now you're attributing claims to me I didn't make. We're perfectly fine hypothesizing about the origin of the first cells, where did I say otherwise?
As long as we make sure that we are honestly and openly stated that we're hypothesizing, that's actually totally fine with me.
Looking at the history of science lends zero credibility to a supernatural origin of life
Only to anyone who’s either never created anything or has absolutely zero knowledge of engineering systems.
You didn't understand what I just wrote. The history of science = no supernatural events ever discovered. Ever. Not once. Look at that list of phenomena that used to be the arena of the supernatural. ALL nature, ALL of it.
It would seem you're holding out hope for something with infinitesimally small odds. It reeks of nothing but religious faith at this stage. But let's be honest, that is really what this is all about to you. You believe in a supernatural designer, that's why you believe it did supernatural designing despite all the evidence we have accumulated from the real world that none of the observed phenomena were ever due to the supernatural.
So here you are now, with the next big gap in scientific knowledge, and you're still betting on the supernatural. The rest of us got the picture a loooong time ago.
But to anyone who does, the universe in general, and life in particular SCREAMS of design. Alas, but I see that you've conveniently ignored that and just skipped to asserting what you're trying to prove.
It's a probabilistic argument, also called statistical syllogism, or bayesian reasoning. I'm not assuming or asserting, I'm calculating the odds that the future will be different from the past in this respect. There is very very little reason to think it will be. Everything else so far explained has been physics and nature, there's very little reason to think this picture is going to change any time soon.
Thanks for your time.
Rumraket:
DeleteWe see irreducibly complex systems arising constantly through physics alone.
Uh, no. Unfortunately for your argument, the 2nd law of thermodynamics along with the pesky notion of probabilities flatly refutes that claim.
I did [account for the genesis of the first cell], it's just physics
Nope, not without the intervention of an intelligent agent to overcome that darned 2nd law…
There are four fundamental forces of physics, they are constantly in effect between the basic subatomic constituents of the cell.
And they all obey that danged 2nd law. :(
Whatever the cell does, it does because of the properties of it's constituents.
And it has been demonstrated over and over that the arrangement of those constituents (read DNA) could not have randomly self-assembled—the universe ain’t old enough.
Nope, I told you how a cell comes about through natural means.
No, you didn’t tell me how a cell comes about. Sorry, but in educated circles, blithely asserting, “That's how nature and the material world works,” as an explanation of how the first cell formed is, um, frowned upon—you know, not very sciency.
Keep up this nervous, feeble damage-control.
I’m not nervous and unlike, “whatever the cell does, it does because of the properties of it's constituents,” my arguments aren’t feeble.
The history of science = no supernatural events ever discovered. Ever. Not once.
With the possible exceptions of DNA, consciousness, reason…
It would seem you're holding out hope for something with infinitesimally small odds.
I am???
It reeks of nothing but religious faith at this stage.
Uh, the only thing reeking here is your religiously atheistic and blind faith that DNA managed to self-assemble with just the right sequence.
So here you are now, with the next big gap in scientific knowledge, and you're still betting on the supernatural. The rest of us got the picture a loooong time ago.
This is surreal. Will you ever see that it’s your worldview with the gaping holes in it that science simply can’t overcome?
It's a probabilistic argument
YES! When it comes to the phenomenon of DNA, it absolutely is. Your worldview has zip, zero, nada explanation for its “naturalistic” origin, yet you stupidly cling to the non-existent hope that someday science will find one. When will you accept the fact that the probabilistic numbers and the exquisitely fine-tuned physical laws of the universe are simply not on your side?
Nope, not without the intervention of an intelligent agent to overcome that darned 2nd law…
DeleteDo you really think physics (or God, or whatever) exempts "intelligent agents" from the Second Law? Intelligent agents can exist despite the Second Law, because they are not isolated systems. Like life in general, and like other "irreducibly complex" systems, they use natural energy flows to stay away from thermal equilibrium. Physics does not prohibit self-organisation, as long as it can draw low-entropy energy from the environment. Starve it, and it will die in full accordance with the Second Law.
JCC, the argument about the Second Law of Thermodynamics is like believing you're Napoleon. The 2LOT argument should be a topic of study for psychologists, experts in abnormal psychology.
DeleteIt's one of the most egregiously dishonest lies in the history of creationism, and that's saying something.
2LOT says nothing, nothing at all, about irreducible complexity. Like all creationists, you just lie about what 2LOT says.
It's also batty to argue that "intelligence" can violate or "get around" 2LOT. If that were true, engineers could violate 2LOT and design a perpetual motion machine, and transfer heat from colder objects to hotter ones. Solve the energy crisis. More than a hundred years of experiments falsify that. "Intelligence" cannot violate 2LOT.
2LOT says that if a system radiates a heat delta Q to its environment, it is PERMITTED an entropy decrease of deltaS if deltaS <= delta Q / T, where T is temperature. To this you add corrections for matter leaving or entering a system.
For the special case of an isolated system, delta Q = 0, so delta S < = 0. That's a special case, and it doesn't apply to living things, because they radiate a lot of heat.
Living things radiate heat, so delta Q > 0, and that means 2LOT explicitly PERMITS living things to go to lower entropy.
2LOT says nothing about information, complexity, machinery, teleonomy, purpose, intelligence, or irreducible complexity. All creationists just lie about it and say 2LOT says whatever they want it to say.
You introduce this argument because you're losing, badly.
The creationist travesty of the Second Law of Thermodynamics, in three acts:
Delete(I) Entropy must unconditionally increase in the absence of intelligent agents.
(II) Intelligent agents (and only they) have a special licence from God, so they can cause entropy to decrease.
(III) Entropy = disorder (it follows that ordered complexity can't emerge spontaneously).
Piotr GÄ…siorowski:
DeleteDo you really think physics (or God, or whatever) exempts "intelligent agents" from the Second Law?
No, and I didn’t say they were. I said they were “able to overcome it.” Nice try at deliberately ascribing a false meaning to my words.
We see irreducibly complex systems arising constantly through physics alone.
DeleteUh, no. Unfortunately for your argument, the 2nd law of thermodynamics along with the pesky notion of probabilities flatly refutes that claim.
Yes we do, every time a cell divides this is what happens. A new irreducibly complex entity is being created by the laws of physics. Every single one of those atoms and molecules the new cell is made of are ALL subject to the laws of physics, INCLUDING the 2nd law of thermodynamics.
It's obvious you don't understand thermodynamics, including the argument I'm making.
I did [account for the genesis of the first cell], it's just physics
Nope, not without the intervention of an intelligent agent to overcome that darned 2nd law…
Nothing overcomes the 2nd law. Everything is subject to it. But thank you for reaffirming that the origin of the first cell can't have been a supernatural event, but just another natural and physical event.
All it takes to reduce entropy is the conversion of usable energy into less usable forms. This is how complexity is built by the laws of physics, therefore the 2nd law isn't "overcome", because the net entropy of the system still increases (because of that pesky conversion of usable energy into less usable forms). This is true whether it is a human designer, or just a complex weather pattern doing the "designing". It's still just physics, it's still subject to the 2nd law, it still happens at the conversion of usable energy into less usable forms. Yes, human beings convert energy into less usable forms too. We are natural entities just as well as anything else, we must take in energy and convert it into less usable forms.
You seem to have shot yourself in your foot when you say the designer also had to be subject to the 2nd law of thermodynamics. That must mean it's a natural designer. Like an alien.
There are four fundamental forces of physics, they are constantly in effect between the basic subatomic constituents of the cell.
And they all obey that danged 2nd law. :(
Yes, and when there is conversion of usable energy into less usable forms, there can be a rise in complexity - though the net entropy of the whole system still goes up(because of this conversion).
It's clear you don't understand how thermodynamics and the 2nd law relates to life. I recommend a book I recently read myself: "Into the cool - Energy flows, Thermodynamics and Life"
Whatever the cell does, it does because of the properties of it's constituents.
DeleteAnd it has been demonstrated over and over that the arrangement of those constituents (read DNA) could not have randomly self-assembled—the universe ain’t old enough.
DNA didn't randomly self-assemble, there is evidence that the biochemical pathways responsible for synthesizing DNA monomers evolved from RNA precursors.
When you liken the origin of life to "random self-assembly" it is clear you have very little grasp of the actual subject or any of the current research going on. Nobody actually believes that a complete cell just randomly self-assembled in one fell swoop as if by a miracle of nature.
There's a pretty long process of chemical evolution happening before any of the things we reckognize from extant life (such as DNA, RNA and large complex proteins) make their way onto the scene through this evolutionary process. I recommend taking a look through this guys's recent publications:
Selected Publications by Michael Russell
I recommend in particular the paper "Beating the acetyl coenzyme A-pathway to the origin of life
doi: 10.1098/rstb.2012.0258
You'll find nothing reminiscent of "random self-assembly" of a complete functional modern-like cell in there. You'll find a lot concerning natural cycels, thermodynamics of geochemistry, abiogological chemical pathways that resemble biological metabolic pathways, semipermeable inorganic membranes etc. etc.
Stop getting your science information from religious apologists with an agenda. Go straight to the source, the scientists actually doing the work. They're not idiots, of course they don't think the whole thing just randomly self assembled. That's just dumb. But there are people out there who stand to benefit from convincing you of this, stop getting your information from these people. They're not worth your time.
You have so many misconceptions about what scientists actually believe surrounding DNA and the origin of life. This isn't necessarily your own fault, you like to read what you find interesting. The trouble his that the people you've been reading haven't been honest to you, they have fed you silly one-liners designed to make scientists working on the origin of life look like silly deluded, atheistic boogeymen out to destroy god (whom they hate).
DeleteI cannot emphasize this enough. Stop getting your science information from people with an agenda. I reckognize it can be difficult to tell them apart, but when in doubt, go straight to the source. Get off ENV and Uncommon Descent, Heck, get off sandwalk if you must, go straight to the source:
Scientists who ACTUALLY WORK on the origin of life. Who do research on the subject, who construct and design the experiments. Read their papers, not popular articles or "spin" constructed by people who have an interest in sensationalizing or dismissing their findings. You'll find these scientists are usually much more honest in their papers (particularly when they have been published in reckognized journals with a good peer review system).
Nobody believes a cell, complete with a functional DNA genome and large complex enzymes, just randomly self-assembled. Nobody.
jcc: I said they were “able to overcome it.”
DeleteNobody and nothing in this universe is "able to overcome" the 2LOT. You might just as well say that intelligent agents can overcome gravity because they can climb the stairs. Entropy CAN decrease in an open system, and (as Diogenes has already pointed out) this fact has very little to do with intelligence, design, complex specified information, or any mystic misreading of physical concepts.
Piotr wrote:"Entropy CAN decrease in an open system, and (as Diogenes has already pointed out) this fact has very little to do with intelligence, design, complex specified information, or any mystic misreading of physical concepts."
DeleteAnd that's my friends is why we are not surprised when tornados run backwards, because the Earth is an open system, tornados derive their energy from the sun, and while turning rubble into houses and cars represents a decrease in entropy, the increase in entropy outside the Earth (in the sun) far exceeds this decrease... ;-)
A tornado itself is actually a nice example of a dissipative structure, that is, of spontaneous self-organisation.
DeleteThe order in tornados and crystals can easily be understood by naturalistic processes, the same does not go for the order of base pairs in DNA.
DeleteBecause? Ah yeah, because you say so.
DeleteAny particular tornado is just as improbable as any long stretch of DNA. No two tornadoes are exactly the same, they're all unfathomably improbable and the odds are, once it has dissipated - no other tornado will ever be ordered exactly like it at any arbitrarily picked moment in time.
DeleteAre we now to conclude nature can't produce tornadoes? That every particular tornado is designed and sustained by an invisible weathergod? Of course not.
So the origin of DNA(or RNA, or whatever came first) here is just another argument from ignorance because we simply haven't yet found the natural process that makes it.
Rumraket wrote: "Any particular tornado is just as improbable as any long stretch of DNA."
DeleteWell there's an argument from ignorance if I ever saw one...
It's a fact. What ignorance are you talking about in particular?
DeleteHow big is the average tornado? How many atoms is it made of? When a tornado rolls across the landscape it picks up material from the ground and the surrounding air. At any given point in time, the tornado will be filled with debris(which can be everything from sand and dust, to blades of grass, lumps of dirt, pieces of rubble and broken buildings, abandoned cats.. you name it) and air molecules (this is what the tornado is made of, of course).
At any given particular moment in time, all those pieces of debris will be distributed throughout the tornado in some particular manner. All the atoms they're made of, all the dust, sand and all the rest of it. I could go on and on about the particular shape of the tornado, the exact distribution of pressure, temperature and wind velocity at all locations inside the tornado. The tornado, whichever tornado at any moment, is incalculably improbable. There will never be another tornado exactly like it, picking up the exact same debris, distributing it throughout an exactly similar tornado in the exact same manner.
There's really no reason to go on. Any particular tornado at any given moment is a unique event that will never be repeated in the lifetime of the universe and it's really simple to see why this is. No two areas are exactly alike, the winds blowing across them will therefore never be exactly alike, the debris they pick up will never be exactly alike, and so on and so forth. There will always be minor differences.
And yet tornadoes happen frequently, and it's just physics.
Why should DNA be any different? We've already established that improbability is not a barrier to the creative power of physics.
Rumraket, does a tornado need need to be very specific to be functional? What about a gene? Can you shuffle around the base pairs any given way and still get a functional protein fold?
DeleteThose are rhetorical questions and you don't need to answer them, but i hope you can see that your analogy is irrelevant.
Furthermore, the physics of tornados is well known while only people with a teleological inclination claim that the arrangement of the DNA follows any physical law.
does a tornado need need to be very specific to be functional?
DeleteFortunately, yes. They don't form easily. Otherwise we would be hit by tornado after tornado.
What about a gene? Can you shuffle around the base pairs any given way and still get a functional protein fold?
Who says we can? You can destroy the functionality of a protein in this way, you can turn a gene into a pseudogene which doesn't encode for anything any longer, you can accidentally produce a new protein which will be co-opted in a new function... so what?
Furthermore, the physics of tornados is well known while only people with a teleological inclination claim that the arrangement of the DNA follows any physical law.
Gobbledygook. "People with a teleological inclination" are those who see function and purpose in everything. Look in a mirror, and you'll see a bloke with a teleological inclination. DNA sequences don't follow any "physical laws" because the laws of physics aren't concerned with such sequences. Any sequence is possible, and none is prohibited by physics.
Piotr, glad that we now agree that base pair sequence does not depend on physical law as a posed to crystal formation and tornados.
DeleteI see that you also agree on the importance of specific complexity in the genes even if you did not quite get my point in contrasting it with the mere complexity of the tornado. This seems also to be Rumraket's problem.
When it comes to teleology, there are so many definitions that based on the problems explaining the simple issues above I will not get in to that, suffice it to say that it should be every mans prerogative to define what he believes, i.e. don't try to tell me what I see in the mirror.
Piotr, glad that we now agree that base pair sequence does not depend on physical law as a posed to crystal formation and tornados.
DeleteThe laws of physics make a DNA molecule possible. It's an aperiodic polymer, and the laws of physics have nothing to say about the order in which the different nucleotides are arranged. They allow the order to be arbitrary, ahich is precisely why that particular molecule can encode information. If the order depended rigidly on the laws of physics, DNA would have no "memory". I think you may rest assured Rumraket knows that.
But tornadoes also have specific and unpredictable individual features which depend on various accidental factors are not required by the laws of physics for a tornado to function. Tornadoes don't make copies of themselves, so they need no dedicated memory.
Piotr wrote" If the order depended rigidly on the laws of physics, DNA would have no "memory". I think you may rest assured Rumraket knows that."
DeleteAll I can say is if he knew, then his analogy with tornados does not make any sense.
Yesterday you did not want to concede the point that tornadoes and crystal formation is easily understood by naturalistic processes as a posed to DNA base pair sequences...Just out of curiosity, what made you change your mind?
I didn't change my mind. There is no contradiction between "The order of nucleotides in DNA is arbitrary and not regulated by the laws of physics" and "The process of DNA formation and replication is 100% naturalistic". The so-called laws of physics are our mathematical descriptions of some fundamental and recurring regularities of the Universe. They are neither meant nor expected to account directly for everything in it. What's important is that DNA sequences don't contradict or defy any laws of physics, and there's nothing in them that suggests a non-naturalistic origin.
DeleteYour trying to twist what the discussion was about. I don't deny that evolution, which I suppose that you refer to, is a naturalistic process but how could you claim that it's as easily understood as a physical law? Even Larry in a recent post wrote "Some of us spend a lifetime trying to understand evolution. We read books, go to meetings, study the scientific literature, and consult experts. It's a difficult subject."
DeleteRumraket, does a tornado need need to be very specific to be functional?
DeleteHow specific is very specific? The total number of possible microstates outnumber the number of "tornado" microstates to an incalculable degree. Tornadoes ARE very specific, they're ALL specific, every single one of them.
What about a gene? Can you shuffle around the base pairs any given way and still get a functional protein fold?
That depends on the protein and what it's doing. It also depends on the environment of the organism. What may be a misfolding piece of junk of no value for a bacteria living inside a hydrothermal vent might be critical to the function of a human skincell. Reality is rarely as simple as "function or not?". Well, it depends.
We have examples of proteins that can change in almost their entire sequence and still adopt a highly similar fold that functions in in a highly similar way
We have examples of proteins that can change almost their entire sequence, adopt a totally different fold but still retain the same function.
We have examples of proteins that can change in the entire sequence but adopt a totally different fold, and do something completely different.
I'd be happy to give you references for all of those. So the answer is "it depends", some things are more constrained than others. Some things are constrained for historical reasons (examples would be tRNA and the Ribosome who have to interact with each other. We could imagine both structures being different at some point in the past, but they have sort of "set in" the way they are and have changed very little, again, for historical reasons in the ancient past) rather than some intrinsic physical constraint, though we have examples of those too (fat soluble proteins have certain intrinsic constraints in common that make them capable of interacting with fat in a way that make them soluble, but there are many solutions to fat-solubility, they're not all identical).
Those are rhetorical questions and you don't need to answer them, but i hope you can see that your analogy is irrelevant.
Not at all, I have quite clearly demonstrated that physics give rise to extremely improbable things. Including tornadoes.
Furthermore, the physics of tornados is well known
That is exactly my point. We don't yet know how life arose, if we did, this debate wouldn't take place (I hope for certain people's sanity's sake). That is exactly why ID is an argument from ignorance.
while only people with a teleological inclination claim that the arrangement of the DNA follows any physical law.
Well, technically it does. You see, any stretch of DNA inside any one of your cells was made by a DNA polymerase enzyme, a physical molecule subject to the laws of physics.
The DNA polymerase attaches to a strand of DNA and copies the sequence, not because it is sentient and can "read" (there are of course no actual letters inside your cells as I'm sure you know), but the chemical interactions that take place between the DNA-polymerase enzyme and the physical structure of the DNA molecule being copied, physically affects the polymerase in such a way that it is caused to make a complementary copy. There's no "hidden intelligence" or "supernatural shenanigans" involved in this process.
Even when mutations happen, it's still just physics at bottom, doing it's thing.
All DNA can thus in principle be traced, through the laws of physics, back to the origin of the very first copy of DNA on the planet some >3.5 billion years ago, which you're now telling me did NOT take place as a natural physical event?
Your trying to twist what the discussion was about.
DeleteI am? Gimme a break.
I don't deny that evolution, which I suppose that you refer to, is a naturalistic process but how could you claim that it's as easily understood as a physical law?
You are putting words in my mouth. I did not compare the relative "difficulty" of evolutionary theory and physical theories. I don't know, by the way, what makes you think physics is easy. It only studies the most fundamental, and therefore relatively simple objects and structures -- simpler, at any rate, than those that the life sciences (or even chemistry, for that matter) are interested in. If physics were enough to understand the universe, we would need no other, more specialised, sciences. Physics underlies all of them, of course, but its apparatus has its limitations.
Even Larry in a recent post wrote "Some of us spend a lifetime trying to understand evolution. We read books, go to meetings, study the scientific literature, and consult experts. It's a difficult subject."
Absolutely. All areas of science are difficult if you want to do a good job practising them.
Jcc, don't waist too much time debating Rumraket (space rocket), I stopped reading his arguments when he proposed that general relativity elucidated the processes in the cell. I think that your point about engineers being more able to recognize designed systems than someone without an engineering background is interesting. I have been thinking the same myself when looking at different aspects of biology. I think it takes a tremendous amount of belief to think that it all came about by mindless processes.
ReplyDeleteAndy Wilberforce,
DeleteJcc, don't waist too much time debating Rumraket (space rocket), I stopped reading his arguments when he proposed that general relativity elucidated the processes in the cell.
Yes, but to his credit, he’s actually one of the more civil atheists here.
I think that your point about engineers being more able to recognize designed systems than someone without an engineering background is interesting.
Anyone who is searching for the truth with any sense of objectivity must eventually confront that reality.
I think it takes a tremendous amount of belief to think that it all came about by mindless processes.
Not just belief, but an unsubstantiated and totally blind faith in the veracity of their presupposed materialist worldview.
@ "Wilberforce" (what a joke)
DeleteBozo, yes, I know who you are Clastie, what's it like being irrelevant? Don't you have another sockpuppet you need to make over on rationalskepticism.org?
@jcc
DeleteYou should go read up on probabilistic empirical reasoning. Specifically bayesian reasoning. I recommend watching this video to start with:
http://www.youtube.com/watch?v=HHIz-gR4xHo
Re: "...engineers being more able to recognize designed systems than someone without an engineering background..."
DeleteAs I've posted too many times here already, my 35 years of mechanical design engineering experience showed me that human design (and I think intelligence also) is itself a process of evolution involving:
1) Lots of random trials (Edison's thousands of lightbulb designs; modern Monte Carlo/genetic-algorithm computer simulations such as used to design the current generation of GE jet engines).
2) A selection mechanism (survival of the fittest in the marketplace - Edsels vs. Impalas). (No doubt there are examples of neutral evolution also.)
3) A form of memory to record the more successful attempts (in the case of biological evolution, DNA).
4) Lots of small, incremental improvements over time (e.g., automobiles, phones, computers).
Intelligence as a process for evolving ideas works the same way, in my limited experience, with 86 billion neurons churning out random combinations of simple ideas in the background to occasionally generate new successful ones.
In short, going to hundreds of design meetings has convinced me that there is nothing magic about human design. If IDers really studied both intelligence and design (as they actually work among humans) rather than assuming magic is at work, they might find themselves doing science, instead of standing in its way.
And then there is the use of genetic algorithms applied to engineering design, used to make production schedules, solve facility/location problems, make transportation/vehicle routing plans, enhance system reliability, and much more.
DeleteGenetic Algorithms and Engineering Design
Mitsuo Gen, Runwei Cheng
ISBN: 978-0-471-12741-3
Evolutionary Multi-Criterion Optimization
Lecture Notes in Computer Science Volume 2632, 2003, pp 737-751
Applications of a Multi-objective Genetic Algorithm to Engineering Design Problems
Johan Andersson
Abstract
This paper presents the usage of a multi-objective genetic algorithm to a set of engineering design problems. The studied problems span from detailed design of a hydraulic pump to more comprehensive system design. Furthermore, the problems are modeled using dynamic simulation models, response surfaces based on FE-models as well as static equations. The proposed method is simple and straight forward and it does not require any problem specific parameter tuning. The studied problems have all been successfully solved with the same algorithm without any problem specific parameter tuning. The resulting Pareto frontiers have proven very illustrative and supportive for the decision-maker.
Intelligent and Evolutionary Systems
Series: Studies in Computational Intelligence, Vol. 187
Gen, M.; Katai, O.; McKay, B.; Namatame, A.; Sarker, R.A.; Zhang, B.-T. (Eds.)
2009
Artificial evolutionary systems are computer systems, inspired by ideas from natural evolution and related phenomena. The field has a long history, dating back to the earliest days of computer science, but it has only become an established scientific and engineering discipline since the 1990s, with packages for the commonest form, genetic algorithms, now widely available.
Steve, the automated design systems that you describe are very good at iterating algorithms until they converge to pre-set criteria, i.e. not really the mindless process without goal that evolution is made out to be.
DeleteDawkins have popularized the idea of "climbing mount improbable" by small incremental steps. Douglas Axe has shown that for e.g. two functional folds of protein no such gradual pathway of incremental improvements exists.
Andy, when you say "they converge to pre-set criteria", what you mean is, to quote Jerry Coyne, What happens, as everyone knows who learns introductory evolution, is that, in a given environment, some genes leave more copies than others, usually because they increase the reproductive output of their possessor.
DeleteI believe Larry has commented on Axe's "work":
http://sandwalk.blogspot.ca/2012/09/douglas-axe-explains-molecular-evolution.html
Andy (or should I say Atheistoclast?) writes: "I think that your point about engineers being more able to recognize designed systems than someone without an engineering background is interesting."
DeleteThis is the common, arrogant appeal to fictional authority used by authors at Uncommon Descent: the arrogant claim that "The evidence against evolution is that I'm smarter than you. The evidence is that engineers are smarter than scientists."
There are countless counter-examples; here's one: the engineer Ed Suominen, the author of Evolving Out of Eden, started life as a creationist in an ultra-conservative Lutheran sect, and was de-converted from creationism by his working experience with evolutionary programming.
Oberski above listed some examples of Genetic Algorithms (GA's) that solve engineering problems that humans can't-- there are many, many, many such examples-- there's a vast literature on the subject-- and they are worth hundreds of millions of dollars. ID creationism has produced nothing worth any money. This is sufficient refutation of the claim.
The authors at UD appear to be largely IT professionals and retired engineers who really think they're smarter than the world's scientists, and that their superior intellect is their best evidence against evolution.
I'm not going to trash on ALL engineers, but I'm going to note that this is an appeal to authority. If appeal to authority were valid, we should first ask what scientists think, and 99.9% of them think that anti-evolution claims are bullocks.
JimV here is an engineer, and he points out quite accurately the parallels between human engineering processes and Darwinian natural selection.
I could also add that I have a huge amount of experience writing software-- I believe I've probably written far more lines of code than the average UDder, boasting of his super-intellect because he can write a Linux shell script!
First of all, writing code doesn't take any brains. It's instinctual, like jerking your hand away from a hot stove. Unlike the UDders, I don't offer my experience at writing code as evidence in favor of evolution-- that'd be appeal to authority.
Second, writing code tells you how to recognize a kludges and lack of forethought-- a piece of code originally written for one purpose, which was then later co-opted for a totally different purpose, for which is poorly adapted. I have a lot of experience in biology, particular molecular biology. It's all kludges, systems built without forethought as to what their final use would be, and co-opting of old functions for new environments.
Andy (or Atheistoclast?) writes: Douglas Axe has shown that for e.g. two functional folds of protein no such gradual pathway of incremental improvements exists.
DeleteThis is an outright lie. Axe has never proven any such thing. Douglas Axe's 2000 paper is one about which all IDiots, including Dembski and Luskin, have simply lied about outright, reversing the point of what his data showed.
The claims of Douglas Axe's 2004 paper are likewise grossly exaggerated and debunked here. They tested a mutant, crippled enzyme for ONE biochemical function-- but the IDiots lie about it and say that they've show all normal enzymes have no functions of ANY kind anywhere about them in sequence space!
Axe and Gauger's 2011 paper in BIO-Complexity (ID vanity journal) was a complete joke-- they claimed they were testing evolutionary theory, but didn't model an evolutionary transition, so who cares? Richard B. Hoppe debunked it here. Axe and Gauger and other IDiots just lied about what hypothesis they were testing. Everyone just pointed and laughed. It was explained to them, years previously, that their work had the cousin problem: nobody claims that your cousin morphed into you; they claim that you and your cousin have a common ancestor. Analogously, Axe and Gauger tried to mutate one modern protein into another modern protein by a direct path. Wrong, that's not testing evolution. Testing evolution means you reconstruct the common ancestor, and test the path from the common ancestor to the descendant form. This fact was pointed out to them at an ID conference in 2006(?) years before they published that trash.
What makes it even worse is that since 2006 Joe Thornton's lab has published many papers on the technique of Ancestral Sequence Reconstruction (ASR) which is the right way to reconstruct, and test, real evolutionary transitions. Thornton and co-workers used it in many papers to show how evolutionary transitions occur, step by step, at the molecular level, so we know they're possible. They published the protocol, so anyone can apply the method; but, strangely, Axe and Gauger refuse to try that method, instead doing it the wrong way. I wonder why that is?
In a pathetic attempted rebuttal to Paul McBride's criticism, Ann Gauger argued that they know they're not testing evolutionary transitions, but they don't need to test real evolutionary transitions, because IDers already know that evolution is impossible, so why bother really testing it? They know what the answer WOULD be, what it has to be-- why do all the extra work of doing the right kind of experiment and telling the truth about what you observed? Lying is easier for Axe and Gauger.
KairosFocus at UD expresses the ID mindset perfectly: "it hardly matters if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand"
So admit it: IDiots are allowed to use any number of logical fallacies, and to lie about their own data and observations-- you're allowed, because you already know the "true" answer-- right?
Diogenes, let's first set the record straight, I'm not Atheistoclast and I've never heard of the site Rumraket speaks of.
DeleteSecondly, my remark of engineers being more likely to recognize design simply means that being used to working out solutions to complex problems and always having to do compromises due design restrictions and interdependent factors with opposite optimization may give you a different view of designed products than someone who thinks design is simply about finding perfect solutions.
I've met lots of smart engineers but there are also plenty that are as dumb as a box o rocks...the same goes for scientists I suppose.
Andy says: "I'm not Atheistoclast and I've never heard of the site Rumraket speaks of."
DeleteThen I certainly retract that claim and apologize.
The fact remains, genetic algorithms based on evolutionary processes solve problems and design technology that humans can't, and they're worth hundreds of millions of dollars, and no ID creationist has created anything worth a dime.
Many of us here have experience writing code. Experience writing code or designing electronics is not evidence against evolution.
JimV:
Delete1) Lots of random trials (Edison's thousands of lightbulb designs…
I doubt Edison would tell you each filament he tested was chosen “at random.” A discriminating, forward thinking mind knows better. However, a blind, “undirected process” (talk about an oxymoron), by definition, does not.
there is nothing magic about human design.
Magic? No. Unique? Absolutely. In any way explicable from a materialistic point of view? Not a chance.
they might find themselves doing science, instead of standing in its way.
The only people “standing in the way of science” today are the Darwinist, Thought Gestapo who believe that only they are capable to “doing” science—and anyone who thinks differently is an illiterate baboon who must be silenced...
Thomas Edison, founder of GE where I worked for 35 years, was largely self-taught and even Phd's in his time did not have the understanding of particle physics and quantum mechanics which later transformed material science into more of a predictive rather than trial and error process. So he kept trying things until something worked. One success in self-described thousands of tries may not seem random to you but I'll let the jury decide. Granted, thousands of years of human civilization had already produced some information which may have been useful, just as billions of years of biological evolution has produced standard sets of genes for phenotype development which make the evolution of new body forms less random than it would otherwise be. This rather strengthens than weakens the likeness, to my mind.
DeleteNot magic, but not explicable from a materialistic point of view - sounds like some sort of retreat into semantics to me. Meanwhile, completely materialistic computers are able to defeat human world champions at chess and Jeopardy, and solve design problems as noted above. Also, there is a mathematical proof that no search algorithm can outperform a random search, when averaged over all search landscapes.
Basically what I am saying is that the evolutionary process seems understandable and consistent with everything I see around me, including the design patents I produced for GE, and the independent proof of Fermat's Prime Theorem (the one that says that every prime of the form 4N+1 is the sum of two squares) which I spent a year on. I think basically what you are saying is that you don't understand how design and intelligence work and therefore it is magical - excuse, me, inexplicable by materialistic means.
It occurs to me that we could both be correct, from our different points of view. Where I see the evolutionary algorithms at work, you see magic, magic, magic (as Elaine of Seinfeld would say) (excuse me again, non-materialistic, non-materialistic, non-materialistic).
(I don't mean to imply that I understand every thing about how human brains work, or ever will, but I have a general concept - evolutionary trial and error - which is consistent with what I have observed over my lifetime. Especially in design work.)
@jcc
ReplyDeleteI doubt Edison would tell you each filament he tested was chosen “at random.” A discriminating, forward thinking mind knows better. However, a blind, “undirected process” (talk about an oxymoron), by definition, does not.
Evolutionary algorithms are used in industry as part of a design process to find design solutions human engineers would never even dream about.
Yes, I know designing a program that utilizes an evolutionary process is to do design, but what that program then goes on to do once it works, is evolution. Blind trial and error. It randomly mutates features of the designed object (analogous to random mutation) and then it compares the results to each other to see which one works best (analogous to natural selection.
See for example: Evolved Antenna
See for example: Evolved Antenna
DeleteThat's not an antenna. THAT's an antenna! ;)
Yes, I know designing a program that utilizes an evolutionary process is to do design, but what that program then goes on to do once it works, is evolution.
DeleteLet's be clear about one thing. "Evolutionary algorithms" do not mimic "evolution." They mimic "strong positive natural selection."
There's a big difference. Organisms do not look like they were designed. no designer would make something as ridiculous as a human body.
@Larry Moran
DeleteI agree.
Though technically you could program in a tolerance for neutral or even slightly deleterious alleles, and include a randomness factor in your selection algorithm and you'd get something reminiscent of drift.
Micro: the Himalayas are growing at a rate of about .005 meters per year.
DeleteMacro: Mount Everest is about 8,848 meters high.
My first-approximation engineering estimate: the Himalayas have been evolving upwards for about 1.7 million years. I.e., multiply "micro" by millions of years and you get "macro". Seems reasonable to me, but I'm just an engineer, who has never seen anything - certainly not any human design - poof into existence rather than evolve over time (other than "magic" illusions, that is). So I for one would like to see some evidence of poofing (under controlled, pre-agreed conditions a la the James Randi challenge) before I abandon what all other evidence and reason point me to.
Which, again is:
1) Microevolution exists.
2) The universe is about 14 billion years old , the Earth is about 4.5 billion years old, and life has existed on the Earth for about 3.8 billion years.
3) Therefore macroevolution exists.
The micro-but-not-macro talking point of creationists really is the most stupid of all their arguments. It amounts to the claim that you can count pennies but never reach a dollar, or that you can have steps but never construct a staircase.
DeleteWhere's the magic barrier? When does the limit set in and prevent the accumulation of microevolution into macroevolutionary change?
DeleteWhere, before the dollar, can we no longer add pennies?
Rumraket, asks what stops micro evolution to cumulate to macro evolution. Looking at natural selection you need to have a path of gradual improvements that can be selected. The critique here has been that when you look at irreducible complex systems this path does not exist.
DeleteIf you instead look at genetic drift, then you have to rely on your luck and you are up against staggering low probabilities, refer to e.g. Bill Dembski's writing on this.
I guess most people believe in a combination of genetic drift and natural selection just as I do. I just doubt that it can amount to much when it comes to macro evolution and you could never sell the idea of universal common descent to me.
To clarify my above comment some what (I know some people are very picky here), random mutations provides the variation that gets fixed in a population by means of natural selection and/or genetic drift.
DeleteRumraket, asks what stops micro evolution to cumulate to macro evolution. Looking at natural selection you need to have a path of gradual improvements that can be selected.
DeleteNo you don't, there is literally zero evidence of this. You simply made it up.
Besides, who the fuck says there isn't? Why can't selection continually operate on size, for example? Why can't selection continually operate on limb morphology and joint positions?
You're telling me we shouldn't believe that it could. Why not? Where's the magic barrier?
If you instead look at genetic drift, then you have to rely on your luck and you are up against staggering low probabilities
Again, completely made up. What is supposed to have staggeringly low probabilities exactly? Fixation of alleles under drift? - You're neglecting population size.
What, then?
, refer to e.g. Bill Dembski's writing on this.
What writing in particular of Bill Dembski's deal with micro and macroevolution under drift and selection?
What little work Dembski has done all deals with the chance of producing some stretch of DNA or protein, and has all fallen victim to the same basic fallacy: He treats evolution as random cance with a pre-specified target. He picks, for example, a single complete protein(or a multicomponent structure like a flagellum), and then calculates the odds of randomly producing that specific protein(or structure) in a single grand event.
That's not how evolution works, so we can simply dismiss that crap as useless because it doesn't deal with observational reality. Evolution works with what already exists and modifies it incrementally over time, towards no end in particular, merely something, ANYTHING that works.
What Dembski and all creationists fail to do (because they never do it), is calculate the odds of evolution finding "anything working" - instead of their prespecifying of a particular target.
They have simply never done this. Ever. It's always the same basic fallacy over and over again. They prespecify a target structure and then calculate the odds of it as if produced by a single miraculous roll of a giant gazillion sided die.
Anybody who understands evolution can see right through the fallacy there.
I guess most people believe in a combination of genetic drift and natural selection just as I do. I just doubt that it can amount to much when it comes to macro evolution and you could never sell the idea of universal common descent to me.
I don't care what can be "sold" to you personally. All you're really telling me is that you have a screwed personal epistemology.
Re: "The critique here has been that when you look at irreducible complex systems this path does not exist."
DeleteTo an engineer the answer to this is very simple. To build an arch you can use scaffolding. After the arch is built you can take the scaffolding away since it is redundant, leaving an "irreducibly complex system". The system without the scaffolding is more efficient (uses fewer resources), so removal of redundant parts is something natural selection would favor.
The last I heard, Dembski's probability filter, or whatever he called it, was disproven by the counterexample of shuffling a double deck of cards (104 cards) and dealing them all out - the probability of the resulting sequence being less than his filter value.
"TalkOrigins" (the website) has information debunking all these standard creationist tropes, which go back 20-50 years. Several of them have been abandoned by their creators under challenge from experts, but continue to pop up again. I guess because as poor as they are, they are the best creationism can come up with.
As I have said, claiming that something nature has produced is impossible for nature to have produced (such as a bumblebee's flight) is not an inherently convincing path of reason, because the chances are that billions of years of nature are smarter than a few years of human thinking. It would be better to first demonstrate that non-natural causes exist with controlled, reproducible scientific evidence. For some reason the Discovery Institute does not seem to be willing to spend research funds on this.
sez andy wilberforce: "Rumraket, asks what stops micro evolution to cumulate to macro evolution. Looking at natural selection you need to have a path of gradual improvements that can be selected. The critique here has been that when you look at irreducible complex systems this path does not exist."
ReplyDeleteThat is, indeed, the 'critique'—or at least, it's the 'critique' which Behe presented in his book Darwin's Black Box. If you're thinking of a different 'critique', presented by a different ID-pusher, fine; but Behe's 'critique' is just wrong—and it's wrong in a way that can be understood even by a teenager with a high-school level of scientific knowledge, let alone a trained scientist like Behe.
Behe's argument in DBB can be stated thusly:
1: An 'irreducibly complex' system is one which requires all of its parts to be present and intact in order for the 'irreducibly complex' system to perform its function.
2: An 'irreducibly complex' system which lacks even one of its parts must, by definition, not be able to perform its function.
3: Any 'direct Darwinian pathway' to an 'irreducibly complex' system must pass thru a stage in which the system consists of the-final-system-minus-one-part.
4: Therefore, there is no 'direct Darwinian pathway' by which it's even possible for an 'irreducibly complex' system to be produced.
5: Therefore, evolution flatly cannot produce an 'irreducibly complex' system.
6: Therefore, any 'irreducibly complex' system which exists in living cells must necessarily have been produced by Intelligent Design.
The flaw in Behe's argument: He assumes that the final step in a 'direct Darwinian pathway' must be 'add a new part'. Because if the final step in an evolutionary process is, indeed, add-a-new-part, then sure, the penultimate stage before completion of the system is, indeed, the-system-minus-one-part, and Behe has defined 'irreducible complexity' in such a way that the-IC-system-minus-one-part cannot be functional. That's fine as far as it goes; Behe has demonstrated that a restricted subset of evolutionary processes (namely, those for which the final step is add-a-new-part) are incapable of producing 'irreducibly complex' systems.
What about evolutionary processes outside of Behe's restricted subset thereof?
Add-a-new-part is, indeed, one of the possible steps in an evolutionary process. It just isn't the only such possible step. In addition to add-a-new-part steps, evolutionary processes can also include delete-an-old-part steps, and even modify-an-old-part steps.
If the final step in an evolutionary process is delete-an-old-part, the penultimate stage in stage before completion of the system is, obviously, the-system-plus-one-part. And there is nothing in Behe's definition of 'irreducible complexity' which requires that an IC system fail to function when a new part is added to it.
If the final step in an evolutionary process is modify-an-old-part, the penultimate stage in stage before completion of the system is, therefore, the-system-with-one-modified-part. Now, I will be the first to acknowledge that it's possible that an IC system could, indeed, fail to function if one of its parts is modified… but Behe's argument flatly requires that every physically possible modification to an IC system, every last friggin' one of them, must necessarily prevent that IC system from functioning.
See any problems with Behe's 'critique', Andy?
Cubist, I'm aware of the critique of the critique as explained by you above.
ReplyDeleteYou seem to have shifted the emphasis of the subject away from macroevolutionary change and over to the evolution of irreducibly complex structures. One does not necessarily require the other. Regardless, the objection you level, that there are no selectable intermediates, begs the question. How do you know this?
DeleteSuppose there's some macroevolutionary transition that required the evolution of some new irreducibly complex structure, this is what you think right?
Take the dinosaur-bird transition as an example then. What irreducibly complex structure did this transition require to evolve, and why can't there have been any intermediate selectable route between them? Where's the magic barrier selection can't overcome, and drift is too improbable to deal with? Speaking of drift, what population size are you imagining?
I see a lot of unfounded assumptions built into your objection, but very little support is given for any of them.
sez andy wilberforce: "Cubist, I'm aware of the critique of the critique as explained by you above."
DeleteGroovy. In addition to being aware of said critique^2, do you also understand said critique^2?
Do you realize that said critique^2 is a valid demonstration that Behe's original 'critique' is bullshit?
Do you realize that since Behe's original 'critique' is bullshit, any conclusions drawn from said original 'critique' are, by virtue of the bullshit nature of said original 'critique', unsupported, hence invalid?
In particular, do you realize that any Irreducible-Complexity-cannot-evolve argument which is based on Behe's original 'critique' is just as bullshitty as said original 'critique' is?
So if you tell me: "I'm gonna drive from LA to Tokyo", then I will tell you " you're crazy man, you can't drive there...you have to get yourself a boat" then I guess you would triumphantly show me a map and point to the Hawaiian islands and say "you're so wrong man, look here it's easy I just take H1 from Honolulu and keep heading east"...
DeleteYeah right, groovy is the word!
@ Andy Wilberforce
DeleteYou have a world map of the complete fitness landscape of all genotypes and phenotypes of life in all possible environments?
Analogies are fine if they are congruent with observational reality. Please demonstrate that yours is.
sez andy wilberforce: "So if you tell me: 'I'm gonna drive from LA to Tokyo', then I will tell you 'you're crazy man, you can't drive there...you have to get yourself a boat' then I guess you would triumphantly show me a map and point to the Hawaiian islands and say 'you're so wrong man, look here it's easy I just take H1 from Honolulu and keep heading east'..."
DeleteI'm sorry, this verbiage of yours is an evasive non-response to my questions, not an actual answer to any of my questions. Here they are again:
You are aware of my critique on Behe's 'critique'. In addition to being aware of said critique^2, do you also understand said critique^2?
Do you realize that said critique^2 is a valid demonstration that Behe's original 'critique' is bullshit?
Do you realize that since Behe's original 'critique' is bullshit, any conclusions drawn from said original 'critique' are, by virtue of the bullshit nature of said original 'critique', unsupported, hence invalid?
In particular, do you realize that any Irreducible-Complexity-cannot-evolve argument which is based on Behe's original 'critique' is just as bullshitty as said original 'critique' is?
That's actually not a bad analogy, Andy, though not in the way you intend.
DeleteBehe's strawman conception of evolution requires that travel only occur by car over paved roads. So his argument is similar to someone saying it is impossible to travel from LA to Tokyo because a car can't make the trip, while ignoring the existence of boats and airplanes.