The immune system cross-examination still burns

| 692 Comments

Heh, five years later and Casey Luskin is still trying to refute the immune system cross: http://www.evolutionnews.org/2010/1[…]_042001.html

Never mind that Luskin’s one immunologist, Donald Ewert, admits that most of his colleagues, even his coauthors, are against him and use homology and comparative evidence everywhere all the time; admits that there is a mountain of literature on the evolution of the immune system; and admits (although he barely stammers it out) that there actually is an evolutionary model for the origin of receptor rearrangement in adaptive immunity and that the researchers themselves interpreted this as confirmation of the basic transposon-origins model (although Ewert somehow thinks this was just a “classification” of the RAG genes as bacterial transposons, ignoring, (a) how damned odd that is to find in vertebrate immune system genes and (b) how this was suspected ever since the 1970s and was deliberately tested in the 1990s-2000s).

Ewert’s reply basically boils down to vague denial of vast amounts of detailed work in evolutionary immunology, raw assertions that sequence similarity doesn’t suggest common ancestry (I dare Ewert/Luskin to do a survey of comparative immunologists on that point), and complaints about the literature not being detailed enough. Unfortunately for them, Behe made all these same points at trial. When you make these kinds of claims in the teeth of an entire specialized subfield which refutes you, it’s your credibility that’s shot, on the stand or anywhere else. So, try again. Give us a better, more detailed explanation of the origins of the immune system, Luskin and Ewert. Good luck!

692 Comments

Give us a better, more detailed explanation of the origins of the immune system, Luskin and Ewert.

“We don’t have to match your pathetic level of detail.”

In reality, you’d never get Luskin to say anything that direct.

Is this bit by Luskin the mighty refutation of which Steve P. writes with such reverence and awe? (scratches head) Looks like another own-goal to me.

Kind of like that “pathetic level of detail” bit. Funny how the creos insist on all the details imaginable or MET must be a lie and a scam, but when challenged to meet the same impossible standard it’s time to make like the proverbial tree and leave by the nearest entrance.

The MadPanda, FCD

The MadPanda, FCD said: Looks like another own-goal to me.

Oh, just another round of Pigeon Chess™.

mrg said: Oh, just another round of Pigeon Chess™.

…with the pigeon equivalent of three-year-old children, one supposes. (They change the rules without notice and throw a temper tantrum when they don’t win.)

The MadPanda, FCD

Somebody better call a Waaaambulance for these guys. No one else cares what they are saying.

Well Behe now has five more years of papers to catch up on. Assuming of course that he ever did get around to reading all of the original papers. As the models get more and more detailed and more and more refined, he is really going to get tired having to ignore more and more data. Does anyone think that he is ever going to do any real research in this field? Does anyone think that he is ever going to propose any real alternative? Why would anyone consider him an expert anyway?

At the next trial, assuming he has the guts to show up, why not put one of the transposon origins guys on the stand? You know, one of thuys who actually did collect data and test the hypothesis. Then ask Behe if there is any research on the question. He will have to deny the very existence of the witness who just testified! Of course, no matter what model is proposed or what evidence is presented, he will still claim it isn’t good enough. But that’s not really the point now is it? I’m sure the next judge will understand that as well.

raw assertions that sequence similarity doesn’t suggest common ancestry

Because, uh, it does everywhere else, including microevolution, but doesn’t where evolution didn’t occur. I mean, really. How could it indicate that evolution occurred when it didn’t?

Just because it’s a prediction of evolution (in context) and not the least bit a prediction of design means nothing. Because, you know, the immune system didn’t evolve, so the evidence entailed by evolution is not actually caused by evolution in specific instances where we know it didn’t happen.

So see, it all makes sense.

And one happy consequence of this reasoned position is that the sort of evidence that demonstrates (in context) that language evolution and microevolution occurred simply means nothing with respect to macroevolution. Not that there’s any apparent line between creationists’ microevolution and macroevolution, it has to be there, since the latter never happened.

Glen Davidosn

The immune system cross still burns

hmm, maybe they should talk to John Freshwater about that.

I bet he could make a sweet tatt out of that with a tesla coil.

DS said:

Well Behe now has five more years of papers to catch up on. Assuming of course that he ever did get around to reading all of the original papers. As the models get more and more detailed and more and more refined, he is really going to get tired having to ignore more and more data. Does anyone think that he is ever going to do any real research in this field? Does anyone think that he is ever going to propose any real alternative? Why would anyone consider him an expert anyway?

At the next trial, assuming he has the guts to show up, why not put one of the transposon origins guys on the stand? You know, one of thuys who actually did collect data and test the hypothesis. Then ask Behe if there is any research on the question. He will have to deny the very existence of the witness who just testified! Of course, no matter what model is proposed or what evidence is presented, he will still claim it isn’t good enough. But that’s not really the point now is it? I’m sure the next judge will understand that as well.

Funny – I actually lobbied for this at the time during the Kitzmiller case! But given the time constraints in a complex case, and the challenges in communicating even the level of detail that we did present, the legal team decided it just wasn’t possible. And that was the right decision, I think.

At one point I suggested that we could call the entire biology department from Harvard or somewhere, but the point was made that (a) its much easier, and frankly more authoritative, to just cite the relevant authorities (NAS and AAAS) when you are making a point about what the authorities say; (b) for detailed points you cite the literature, which is what it is there for in the first place; and (c) for communicating complex science to the court, you get people who are good at that sort of thing, who also know the creationism issue, like Kenneth Miller and Kevin Padian.

Ichthyic said:

The immune system cross still burns

hmm, maybe they should talk to John Freshwater about that.

I bet he could make a sweet tatt out of that with a tesla coil.

LOL, my original title did have an unfortunate weird phrasing, I’ve made some edits.

awww, I liked the original.

:)

btw, I consider this to be YOUR day, Nick, and while we have disagreements about many things, I have to give you a hat-tip for Dover.

The background work you did there was instrumental, I think.

You simply cannot receive too many kudos for it.

Ichthyic said:

btw, I consider this to be YOUR day, Nick, and while we have disagreements about many things, I have to give you a hat-tip for Dover.

Yeah. A round of applause for NM and of course Eugenie Scott.

Is Donald Ewert any relation to Winston Ewert, the grad student at Baylor who has sadly fallen in with a bad crowd?

Glen Davidson said: Just because it’s a prediction of evolution (in context) and not the least bit a prediction of design means nothing.

Every possible outcome is an equally valid prediction of design.

Jason Lisle, talking about recent astronomy discoveries here, said something that I think captures ID’s can-accommodate-any-discovery pablum perfectly. In speaking about large gas giants in very close orbits around other stars, he commented that the discovery “…is perfectly consistent with the creative diversity we expect from the Lord.”

That’s what makes it science, don’cha know.

“…is perfectly consistent with the creative diversity we expect from the Lord.”

…but of course evolution is TOO creative and diverse for his Lord.

Ichthyic said:

awww, I liked the original.

:)

btw, I consider this to be YOUR day, Nick, and while we have disagreements about many things, I have to give you a hat-tip for Dover.

The background work you did there was instrumental, I think.

You simply cannot receive too many kudos for it.

Absolutely. Thanks Nick, for all your efforts in defending evolution. Don’t let the butt heads win.

Merry Kitzmas. And a Festuvus for the rest of us.

Just Bob said:

“…is perfectly consistent with the creative diversity we expect from the Lord.”

…but of course evolution is TOO creative and diverse for his Lord.

When I first read that, I interpreted it as “evolution is also creative …” (something like a schoolyard taunt - my apologies) rather than as “more (in the line of creativity and diversity) than what his Lord is able or willing to do”.

The question arises from time to time, in asking for a description of what happened, according to creationism/intelligent design: What did not happen (or could not, or would not, or will not, or ought not). I suppose that the answer is: evolution. Evolution is the “rock too heavy”.

TomS said: The question arises from time to time, in asking for a description of what happened, according to creationism/intelligent design: What did not happen (or could not, or would not, or will not, or ought not). I suppose that the answer is: evolution. Evolution is the “rock too heavy”.

Given that the fundamentalist movement is heavily bound up in politics, we can probably think of a host of other things they would claim are not ‘consistent with the creative diversity of the Lord.’ I’ll start the list off with two of the most obvious: AGW and gay marriage.

Though I probably shouldn’t blame them for this schtick - its much older than they are. Trying to bolter one’s argument by claiming your opponent is not disagreeing with mere mortals, but with GOD has a long history predating these yahoos. Its the religious variation of “if you can’t pound on the evidence, pound on the table.”

I haven’t listened to the podcast, but just reading the excerpts by Luskin, Ewert’s critique seems to make little sense. First of all, any summary of the argument for the evolution of the adaptive immune system as a simple claim that similarity = homology = proof of evolution has already missed the bus. The point we made here at PT and was later made at the trial is quite different: that by looking at similarities and interpreting them as potential homologies in evolutionary scenarios, scientists could come up with highly predictive non-trivial hypotheses (that the recombination mechanism would actually *work* like transposition, that transposases would be found with high similarity to the immune system enzymes but no immune function, that they would work on sequences very similar to the corresponding immune system sequences, that non-rearranging forms of the antigen receptors would also be found in non-vertebrate organisms, etc) that can be, and were, empirically confirmed. When several multiple predictions of this type are independently confirmed, any honest scientist HAS to conclude that the original hypothesis (i.e. that similarities reflect true homologies) is strongly supported. Compare this to Behe’s passive attitude of “no matter how much we look, we can’t find evidence”, or that the relevant hypotheses were all flights of fancy, or to Ewert’s own “One can easily see how a common ancestor… can equally be replaced by a common designer who used similar structures in different organisms to perform similar functions”, where he not manages to both demonstrate how ID has no predictive value, and to show he understands the evidence perfectly backwards.

OK, I actually listened to the podcast, and it also manages to demonstrate how ID is just an exercise in goalpost-moving. Behe chose the antigen receptor recombination system in the vertebrate immune system as a key example of IC, and based on his broader claim that IC was an insurmountable obstacle to gradual evolution, this was a key part of his argument that the immune system could not have evolved by darwinian mechanisms. He specifically ridiculed the hypothesis that the recombination system could have evolved from transposition systems (the trip in Calvin and Hobbes’ box). Scientists used the same hypothesis he ridiculed to make testable predictions, which were later empirically verified. So Ewert says that what scientists should have demonstrated instead was how the evolution of the *entire immune system* occurred. Ridiculous.

I’ve considered Casey Luskin to be a hack ever since I saw this quote from him trying to rebut the Chromosome #2 genetic evidence for common ancestry between humans and other ape species:

[b]”To be more specific, the fusion-evidence implies that some of our ancestors likely had 48 chromosomes. But Miller has not provided any evidence that the individual with 48 chromosomes was historically related to modern apes. (I grant that our chromosome #2 has banding patterns similar to two ape chromosomes, but given that our chromosome structure is generally similar to that of apes anyways, it is not a stretch to assume that any 48 chromosome ancestor of modern humans might have also had a chromosomal scheme similar to that of apes, regardless of whether or not that individual was related to apes. Claiming that banding pattern similarities is evidence of common ancestry with apes simply invokes the “similarity = common ancestry” argument, and thus begs the question.) It is entirely possible that our genus Homo underwent a chromosomal fusion event within its own separate history.”[/b]

So he thinks “similarity = common ancestry” begs the question? This idea is the whole basis on which the field of genetics is founded! I suppose we should toss paternity tests and DNA evidence for criminal convictions out the window, if genetic similarity can’t be considered evidence of relatedness.

eric said:

Glen Davidson said: Just because it’s a prediction of evolution (in context) and not the least bit a prediction of design means nothing.

Every possible outcome is an equally valid prediction of design.

Jason Lisle, talking about recent astronomy discoveries here, said something that I think captures ID’s can-accommodate-any-discovery pablum perfectly. In speaking about large gas giants in very close orbits around other stars, he commented that the discovery “…is perfectly consistent with the creative diversity we expect from the Lord.”

That’s what makes it science, don’cha know.

It appears he is borrowing a page from your book, Eric. How many times have we heard from posters here commments like “that is not a problem for evolution.” or “How is that a problem for evolution?”

These types of retorts are indicative of your (pl) penchant for interpreting any and all data to fit your preconceived notions of non-directed, non-designed, unseen step-wise fortuitous accumulations of extremely rare beneficial mutations building complex, multi-tier, interactive systems over deep time.

Thing is, it is not possible to provide supporting evidence for non-direction, non-purpose, non-design. Moreso, such a philosophy flies in the face of what we as humans experience in our daily activity.

In your (pl) own words, it is simply wrong-headed to think there is no design and no purpose. It is all that we see in the microscope and on the street.

Two errors here with Steve P’s claims:

These types of retorts are indicative of your (pl) penchant for interpreting any and all data to fit your preconceived notions of non-directed, non-designed, unseen step-wise fortuitous accumulations of extremely rare beneficial mutations building complex, multi-tier, interactive systems over deep time.

No, this is not the case. There are things Design can easily do, that descent with modification simply cannot do. There is in fact a vast difference between a narrowly range of incremental possibilities, and an infinite range of non-incremental changes. The Designer could easily put a rabbit in the pre-Cambrian. Evolution can’t.

In your (pl) own words, it is simply wrong-headed to think there is no design and no purpose. It is all that we see in the microscope and on the street.

Yes, of course there is design and purpose, and we see it in the microscope and on the street. The question isn’t whether or not there is design or purpose (or functionality), the question is how it got there, what mechanism(s) led to it. Even Bill Dembski had to admit (before he decided to censor the whole discussion away!) that natural selection leads to designs, makes “intelligent” choices (between which organisms survive and which do not), that there is in fact direction and purpose (differential rewards for fitting ecological niches, etc.)

So evolution, unlike Divine Design, is highly limited in where it can go and and how it can get there from here. But if staying alive to breed another generation is considered a purpose, and living in a way that accomplishes that is considered a function, then indeed there is design and purpose in nature. No external imaginary entities required.

Steve P. said:

eric said:

Glen Davidson said: Just because it’s a prediction of evolution (in context) and not the least bit a prediction of design means nothing.

Every possible outcome is an equally valid prediction of design.

Jason Lisle, talking about recent astronomy discoveries here, said something that I think captures ID’s can-accommodate-any-discovery pablum perfectly. In speaking about large gas giants in very close orbits around other stars, he commented that the discovery “…is perfectly consistent with the creative diversity we expect from the Lord.”

That’s what makes it science, don’cha know.

It appears he is borrowing a page from your book, Eric. How many times have we heard from posters here commments like “that is not a problem for evolution.” or “How is that a problem for evolution?”

These types of retorts are indicative of your (pl) penchant for interpreting any and all data to fit your preconceived notions of non-directed, non-designed, unseen step-wise fortuitous accumulations of extremely rare beneficial mutations building complex, multi-tier, interactive systems over deep time.

Thing is, it is not possible to provide supporting evidence for non-direction, non-purpose, non-design. Moreso, such a philosophy flies in the face of what we as humans experience in our daily activity.

In your (pl) own words, it is simply wrong-headed to think there is no design and no purpose. It is all that we see in the microscope and on the street.

Sorry, but eric’s claim that “Every possible outcome is an equally valid prediction of design.” is such a BIG LIE that it’s not even phunny. Just stupid. Unless he is admitting that the Designer he beleives in is an incompetent idiot. After all, men do tend to create God in their own limited image.

And everything Steve P. said to support eric was bull$#it too. Science has no preconceptions. We go where the evidence leads us. Our ancestors may have assumed life was a product of Intelligent Design just because they were ignorant about how else it could have come about. Once natural selection was understood to be a force capable of changing lines of organisms over millions of years, Intelligent Design as a credible scientific theory was debunked. The only way it could be resurrected was to show that all organisms designed are perfect in how they are made and how they function. We know that’s not true. When we look closely at things like the three chambered hearts of amphibians or whales having lungs but no gills, for example, we know how clumsy and limited natural selection is. It works, but barely. Hint: Contrary to popular belief, evolution does not operate by the survival of the fittest, but by the reproduction of the fit enough.

Sorry, but eric’s claim that “Every possible outcome is an equally valid prediction of design.” is such a BIG LIE that it’s not even phunny. Just stupid.

I have to defend Eric. Unless you can point to anything whatsoever and say “this could not have been designed this way by divine miracle”, he’s quite right. Theistic evolutionists (those who believe evolution is their god’s chosen means of achieving His Purposes) still impose this notion of “if it happened this way, that’s because it was meant to by external influence.”

(And I must say I’ve seen no mechanical or procedural limits to what “goddidit” can be applied to.)

Flint said:

Sorry, but eric’s claim that “Every possible outcome is an equally valid prediction of design.” is such a BIG LIE that it’s not even phunny. Just stupid.

I have to defend Eric. Unless you can point to anything whatsoever and say “this could not have been designed this way by divine miracle”, he’s quite right. Theistic evolutionists (those who believe evolution is their god’s chosen means of achieving His Purposes) still impose this notion of “if it happened this way, that’s because it was meant to by external influence.”

(And I must say I’ve seen no mechanical or procedural limits to what “goddidit” can be applied to.)

You left out the other part of my statement against eric: “Unless he is admitting that the Designer he beleives in is an incompetent idiot. After all, men do tend to create God in their own limited image.” I can believe in an Intelligent Designer who made all of life, but he wouldn’t be worthy of my worship, because he would be quite inferior in creative ability to me. I also don’t beleive in the Bible as the Word of God for simular reasons.

??? I don’t think eric believes in any Designer. He is pointing out that the creationist Designer is logically unconstrained by any limitations whatsoever. And that therefore, logically, ANY CONCEIVABLE outcome could have been Designed. And that therefore, logically, Design cannot make any prediction that can turn out to be incorrect in any way. Which makes every possible outcome a valid prediction of Design, just as eric said.

Yes, of course there is design and purpose, and we see it in the microscope and on the s treet. The question isn’t whether or not there is design or purpose (or functionality), the question is how it got there, what mechanism(s) led to it. Even Bill Dembski had to admit (before he decided to censor the whole discussion away!) that natural selection leads to designs, makes “intelligent” choices (between which organisms survive and which do not), that there is in fact direction and purpose (differential rewards for fitting ecological niches, etc.)

It seems you are ascribing something to natural selection that is simply not there. NS is an outcome. Nothing more. NS doesn’t do anything whatsoever. The doing comes from the organism.

So evolution, unlike Divine Design, is highly limited in where it can go and and how it can get there from here. But if staying alive to breed another generation is considered a purpose, and living in a way that accomplishes that is considered a function, then indeed there is design and purpose in nature. No external imaginary entities required.

Staying alive is never a question for life in general. It only seems to be a question for individual members of species with longer gestation periods and lower reproductive numbers.

At any rate, survival as a purpose is trivially true. But what I am talking about is purpose as quality decisions, detached from questions of survival.

This is what Man does. I don’t consider my (physical) survival when I decide to attend Church on Sunday, or buy a Mitshubishi instead of a Toyota, or Reebok Zigtech instead of Nikes, or coffee instead of Coke, or helping a tourist with directions even though I am late for work, or putting a bill in a tin cup, or countless other examples of purpose detached from physics and chemistry.

It seems you are ascribing something to natural selection that is simply not there. NS is an outcome. Nothing more. NS doesn’t do anything whatsoever. The doing comes from the organism.

This needs to be clarified a bit. NS refers to the environment’s filtering effect. Some organisms make it through the filter, others do not. Kind of like a tough school where a few students graduate and most flunk out. If only those who graduate are permitted to have children, after a few generations one would expect the average student to produce better schoolwork, right? The environment can be a tough school.

Staying alive is never a question for life in general. It only seems to be a question for individual members of species with longer gestation periods and lower reproductive numbers.

I don’t know what you mean by this. There are multiple strategies in nature that have proved (by surviving) to be effective. One strategy is long gestation periods, and careful protection of the offspring. Another is producing vast numbers of offspring very few of which will survive to breed. Another is having offspring extremely early in the life cycle (pregnancy before hatching, even). Staying alive is HARD, but many strategies are workable. Staying alive is an issue for ALL life, regardless of the various strategies that have evolved.

At any rate, survival as a purpose is trivially true. But what I am talking about is purpose as quality decisions, detached from questions of survival.

But even that would seem to be universal. Nearly all organisms, even bacteria, make “quality of life” decisions like avoiding danger, moving toward food, etc. Sexual species make decisions about who gets to mate, etc.

This is what Man does. I don’t consider my (physical) survival when I decide to attend Church on Sunday

Nor does my cat seem concerned with physical survival when it decides to play with a ball of yarn, or curl up in my lap. So it might very well be the case that all organisms have some notion, at some level, of what makes THEIR life worth living.

And for nearly all of your (and my) species history, the immediate goal of staying alive dominated their lives continually. Most offspring did not live to breed for most of that time, most of those who did just barely made it, and life was indeed cruel, brutish and short. There are genetic clues that our species went through some bottlenecks of near-extinction.

Yes, recently (and mostly with the advent of science) we have abstracted the need for survival somewhat so we can enjoy our lifes rather than just staying alive. But we are no smarter today than we were 50,000 years ago. We simply managed to invent means of making our lives easier.

In context of this OP, there are so many questions that darwinian concepts can’t answer IMHO that is seems so presumptuous to put all ones eggs in that basket.

How does one come to the conclusion that the immune system is not a designed system? To answer that question you have to delve into the deep history of life and answer such threshold questions as:

1) how did organisms recongize other organisms as sources of energy?

2) how did these organisms manage the consumption of other organisms when their structure was made for consumption of nutrients directly from the environment?

3)how and why did some organisms become pathogenic?

4)Why are some organisms both symbiotic and pathogenic?

5)How did organisms recognize the difference between symbiotic and pathogenic organisms?

It appears you have to have a rudimentary immune mechanism in place in order to recognize a threat. As well, having even a rudimentary immune mechanism in advance of a threat is foresight.

So the chicken/egg problem of the immune system in particular and other systems in general seems an insurmountable problem from a non-purpose, non-design perspective.

Steve P. said: The split gene theory is a radical departure from the current Darwinian narrative.

I have no idea what paper you read, but it wasn’t the one you linked to. For the lurkers, here’s the author’s summary of the paper (I don’t think posting it is a problem, given that its smaller than the abstract and abstracts are regularly released):

This study presents evidence that split genes coding for highly complex proteins could have occurred indigenously in a small amount of pre-biotic random genetic sequences, possibly solving the enigma of the origin of biological complexity.

My (albeit brief) reading is that they think bits of random DNA arose in the soup before life did. The first life forms then co-opted it. This is different from what I understand about the standard abiogenesis hypothesis (i.e. DNA evolved first in organisms), but its still an abiogenesis model.

So, when you say:

However, yes IMO the philosophical implications of the split gene theory does in fact favor an intelligent origin, rather than purposelessness.

Could you explain to me how you get ‘intelligent origin’ from ‘indigeneously in a small amount of pre-biotic random genetic sequences?’ Because I have no idea how the latter is evidence of the former.

SWT said:

I have tried, multiple times, to engage several of our trolls in actual discussion. My experience after doing so is that the trolls do not appear to be interested in any sort of discussion; rather, they respond selectively to those who attack rather than to those who attempt conversation.

MANY years ago, on a Usenet group, I let loose my Markov-chain Travesty generator robot on an obnoxious & egregious troll.

Every time the toll posted, the robot replied with a travesty of his post, followed by a response that was a travesty derived from of ALL the troll’s previous posts everywhere on Usenet.

At one point, to the delight of (nearly) all, the troll got into an intense argument with the robot… and lost.

I’ve still got that code around here somewhere… hmm… adapt to web…

Nah, probably not.

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This page contains a single entry by Nick Matzke published on December 20, 2010 7:55 PM.

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