Some help please on refuting ID'sts

[David M]

I've been involved for 2 months in a disucssion refuting ID claims.

http://daily.stanford.edu/comments/2008/1/28/hitchensKnocksIntelligentDesign

I've just been landed with the following article in the usual way of ID arguments, copy-and-paste some rubbish.

http://www.uncommondescent.com/evolution/fishers-fundamental-theorem-of-natural-selection-the-death-sentence-for-darwinism/

If anyone has a little time could they point out some of the most foolish mistakes (I'm sure there are some) as this is not a subject I know much about.

[ck1]

I've been involved for 2 months in a disucssion refuting ID claims.

http://daily.stanford.edu/comments/2008/1/28/hitchensKnocksIntelligentDesign

I've just been landed with the following article in the usual way of ID arguments, copy-and-paste some rubbish.

http://www.uncommondescent.com/evolution/fishers-fundamental-theorem-of-natural-selection-the-death-sentence-for-darwinism/

If anyone has a little time could they point out some of the most foolish mistakes (I'm sure there are some) as this is not a subject I know much about.

Your first link is to really, really long comments thread. Are there particular sections or posts you could highlight?

What is the connection between the two links? The UD link is a long discourse by Sal Cordova (engineering student, YEC and IDist) on his odd notions about natural selection.

[Obd]

I notice that the guy at UD is rather orgasmic about this quote by Michael Lynch:

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer

They happily go on using this phrase as somehow implying the 'death of darwinism', but they seem to misunderstand Lynch. The most important phrase in this quote is 'for all aspects of biodiversity' Lynch has done some work that seems to indicate genetic drift might play a bigger role than hardcore selection fans like to think:

One of the primary goals of our work on gene duplication is to explain the shortcomings of the classical model, which postulates that the usual fates of duplicated genes are either conversion to a nonfunctional pseudogene or acquisition of a new function. We believe that duplicate genes are frequently preserved through a partitioning of functions of ancestral genes, rather than by the evolution of new functions. We have developed methods to estimate the rate of origin and loss of duplicate genes, and we are currently studying the features of newly arisen duplicates that have not yet gone to fixation. In addition, we have recently shown that the modular regulatory-region architecture common in eukaryotes can spontaneously emerge in populations of sufficiently small size. These results challenge the popular idea that modularity arises as a direct consequence of selection for morphological complexity, and by extension raise questions about the common assumption that natural selection was responsible for the emergence of multicellularity.

Furthermore there's a letter to Nature by Lynch in which he states the following:

"Two factors have facilitated the promotion of ID. First, IDers like to portray evolution as being built entirely on an edifice of darwinian natural selection. This caricature of evolutionary biology is not too surprising. Most molecular, cell and developmental biologists subscribe to the same creed, as do many popular science writers. However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity . . . But features of the genome, such as genomic parasites or non-coding introns, which aren't so evolutionarily favourable (nor obviously 'intelligent' innovations), can be more readily explained by models that include random genetic drift and mutation as substantial evolutionary forces.

So, while UD is using Lynch as someone who 'devastates evolution', he's actually merely challenging the absolute role sometimes attributed to natural selection as opposed to, for instance, genetic drift. Note that Lynch agrees that natural selection plays an important role, but that it's simply not an 'all powerful explanation for all aspects of biodiversity'.

Ofcourse selection not being the all powerful explanation for everything might seem huge for someone (say, a creationist) that hasn't been keeping up with evolutionary biology since Darwin, but for someone who has been keeping up this should hardly come as a surprise.

[SteveF]

From Salvador:

If selection for the 4-chambered heart overtakes the population, then the 3-chambered hearts are eliminated (which is definitely not the case since reptilian 3-chambered hearts still exist). If selection for the 3-chambered heart takes place, then 4-chambered hearts are eliminated (which is clearly not the case since mammalian 4-chambered hearts exist).

Of course, one will argue that the two kinds of heart architectures might fall in separate niche’s (either geographically or via other means) and thus we prevent competition between the 3-chambered and 4-chambered heart. But competition is at the heart of natural selection.

Woah that's dumb. It's almost an "if we evolved from monkeys why are there still monkeys argument"

[VoxRat]

I notice that the guy at UD is rather orgasmic about this quote by Michael Lynch:

the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer

They happily go on using this phrase as somehow implying the 'death of darwinism', but they seem to misunderstand Lynch. The most important phrase in this quote is 'for all aspects of biodiversity' Lynch has done some work that seems to indicate genetic drift might play a bigger role than hardcore selection fans like to think:

One of the primary goals of our work on gene duplication is to explain the shortcomings of the classical model, which postulates that the usual fates of duplicated genes are either conversion to a nonfunctional pseudogene or acquisition of a new function. We believe that duplicate genes are frequently preserved through a partitioning of functions of ancestral genes, rather than by the evolution of new functions. We have developed methods to estimate the rate of origin and loss of duplicate genes, and we are currently studying the features of newly arisen duplicates that have not yet gone to fixation. In addition, we have recently shown that the modular regulatory-region architecture common in eukaryotes can spontaneously emerge in populations of sufficiently small size. These results challenge the popular idea that modularity arises as a direct consequence of selection for morphological complexity, and by extension raise questions about the common assumption that natural selection was responsible for the emergence of multicellularity.

Furthermore there's a letter to Nature by Lynch in which he states the following:

"Two factors have facilitated the promotion of ID. First, IDers like to portray evolution as being built entirely on an edifice of darwinian natural selection. This caricature of evolutionary biology is not too surprising. Most molecular, cell and developmental biologists subscribe to the same creed, as do many popular science writers. However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity . . . But features of the genome, such as genomic parasites or non-coding introns, which aren't so evolutionarily favourable (nor obviously 'intelligent' innovations), can be more readily explained by models that include random genetic drift and mutation as substantial evolutionary forces.

So, while UD is using Lynch as someone who 'devastates evolution', he's actually merely challenging the absolute role sometimes attributed to natural selection as opposed to, for instance, genetic drift. Note that Lynch agrees that natural selection plays an important role, but that it's simply not an 'all powerful explanation for all aspects of biodiversity'.

Ofcourse selection not being the all powerful explanation for everything might seem huge for someone (say, a creationist) that hasn't been keeping up with evolutionary biology since Darwin, but for someone who has been keeping up this should hardly come as a surprise.Hey! That sounds highly resonant with certain creationists' quote-mining of Will Provine! (http://www.richarddawkins.net/forum/viewtopic.php?f=46&t=6571&p=114456&hilit=provine#p114456)

[Obd]

Hey! That sounds highly resonant with certain creationists' quote-mining of Will Provine! (http://www.richarddawkins.net/forum/viewtopic.php?f=46&t=6571&p=114456&hilit=provine#p114456)

I remember a topic about that on IIDB too, can't remember who brought it up though.

[David M]

I've been involved for 2 months in a disucssion refuting ID claims.

http://daily.stanford.edu/comments/2008/1/28/hitchensKnocksIntelligentDesign

I've just been landed with the following article in the usual way of ID arguments, copy-and-paste some rubbish.

http://www.uncommondescent.com/evolution/fishers-fundamental-theorem-of-natural-selection-the-death-sentence-for-darwinism/

If anyone has a little time could they point out some of the most foolish mistakes (I'm sure there are some) as this is not a subject I know much about.

Your first link is to really, really long comments thread. Are there particular sections or posts you could highlight?

What is the connection between the two links? The UD link is a long discourse by Sal Cordova (engineering student, YEC and IDist) on his odd notions about natural selection.

The first link is where the "discussion" is taking place. Its this discussion that brought me to RnR and then here. The second link is the one that was just cut and pasted that I want to respond to. I'm sure Cordova has the wrong end of the stick but I'm not knowledgable on the subject other than that he is misrepresenting Lynch. I've already pointed out that Lynch in his book accepts NS as a factor but not the sole factor, which is the point that really he is making with that quote. The UD item 6th post from the end (from Tag Doc) and then my first response 3 from the end.

The ID sock puppets have pretty much stopped trying to post anything from scientific papers as the evo defenders have found it fairly easy to rip their points apart when they do so, it usually the common mistake of finding a supporting quote on AiG/DI rather than reading the paper.

Just one or two points on how Cordova is getting it wrong or pointers on where to find this info would be enough. I've learnt some very interesting things researching answers to the ID arguments over the last 2 months - made me realise how far I'd fallen behind the science over the past few years :)

[Febble]

Interesting comment by Allen MacNeill, here (http://www.uncommondescent.com/evolution/fishers-fundamental-theorem-of-natural-selection-the-death-sentence-for-darwinism/#comment-212246).

No-one has responded it to it yet. And I fear that despite his warning, it will be quote-mined. MacNeill tends to write quote-mineable sound-bytes, unfortunately. But I suppose the upside is that he's managed not to be banned from UD yet.

[Monad]

So, while UD is using Lynch as someone who 'devastates evolution', he's actually merely challenging the absolute role sometimes attributed to natural selection as opposed to, for instance, genetic drift. Note that Lynch agrees that natural selection plays an important role, but that it's simply not an 'all powerful explanation for all aspects of biodiversity'.

Ofcourse selection not being the all powerful explanation for everything might seem huge for someone (say, a creationist) that hasn't been keeping up with evolutionary biology since Darwin, but for someone who has been keeping up this should hardly come as a surprise.

Or even Darwin himself since he never argued it was the sole cause of diversity.

[Obd]

So, while UD is using Lynch as someone who 'devastates evolution', he's actually merely challenging the absolute role sometimes attributed to natural selection as opposed to, for instance, genetic drift. Note that Lynch agrees that natural selection plays an important role, but that it's simply not an 'all powerful explanation for all aspects of biodiversity'.

Ofcourse selection not being the all powerful explanation for everything might seem huge for someone (say, a creationist) that hasn't been keeping up with evolutionary biology since Darwin, but for someone who has been keeping up this should hardly come as a surprise.

Or even Darwin himself since he never argued it was the sole cause of diversity.

True, the key issue here is that creationists seem to have a problem with basic logic. They seem to think that ∃x¬P(x) → ∀x¬P(x) is a valid implication (P(x) being x can be explained by natural selection in this case).

[RAFH]

From Salvador:

If selection for the 4-chambered heart overtakes the population, then the 3-chambered hearts are eliminated (which is definitely not the case since reptilian 3-chambered hearts still exist). If selection for the 3-chambered heart takes place, then 4-chambered hearts are eliminated (which is clearly not the case since mammalian 4-chambered hearts exist).

Of course, one will argue that the two kinds of heart architectures might fall in separate niche’s (either geographically or via other means) and thus we prevent competition between the 3-chambered and 4-chambered heart. But competition is at the heart of natural selection.

Woah that's dumb. It's almost an "if we evolved from monkeys why are there still monkeys argument"

I am not even sure it rises to that level. More like how can you have two kinds of monkeys or fish or how it is possible there could be creatures that use they limbs to swim about and others use their limbs to walk about. Why don't they all have exactly the same limbs and use them then the same way in the same medium. How can there be fish and mammals at the same time, and even worse, amphibian and reptiles and birds as well. The ToE says they should all be the same one kind. It's the babble that says there could be different kinds.

[KCdgw]

Sal snarkily points out that that Lynch hardly mentions Darwin at all in his book. Well, besides the obvious fact Darwin had no clear idea of modern genetics, Sal also 'forgot' to note what Lynch actually had to say:
What would Darwin think of this? Presumably, he would be amazed at how much progress has been made in understanding the genetic basis of evolution, as well as satisfied to see that natural selection has been rigorously validated as the major evolutionary force. But Darwin brought a lot more to the table than natural selection. His greatest contribution was in the promotion of integrative thinking in biology—not the integrative biology sometimes incorporated in the labels of academic departments that exclude entire areas of molecular or cell biology, but a concerted effort to solve problems by bringing together observations from all relevant areas . Darwin did not view all of evolution as being a product of natural selection, and even had a crude idea of random genetic drift: ‘Variations neither useful nor injurious would not be affected by natural selection, and would be left to either as a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions’ (1859)

From page 369 of The Origins of Genome Architecture

KC

[David M]

Thanks for the assistance all of you. Its been 2 weeks now and not a peep from the ID sockpuppets. Looks like evidence has won out over pseudo-science in one discussion.

[supersport]

Interesting comment by Allen MacNeill, here (http://www.uncommondescent.com/evolution/fishers-fundamental-theorem-of-natural-selection-the-death-sentence-for-darwinism/#comment-212246).

No-one has responded it to it yet. And I fear that despite his warning, it will be quote-mined. MacNeill tends to write quote-mineable sound-bytes, unfortunately. But I suppose the upside is that he's managed not to be banned from UD yet.

that is an interesting thread. thanks for posting.

Dr. MacNeil says some interesting things....such as:

Which is precisely why the new focus on phenotypes has revolutionized evolutionary theory. This new focus is relatively immune to both Haldane’s dilemma and to Kimura and Ohta’s theories of neutral and nearly neutral molecular evolution. In other words, focusing on phenotypes recognizes what Waddington recognized almost a half century ago: that changes in genotypes are only weakly correlated with changes in phenotypes.

that's what I've been saying: genetic evolution is uncoupled with phenotypic evolution. This essentially puts natural selection out of a job when it comes to building up populations genetically because if morphology is not tied to changes in genes, then changes in morphology get selected, but it in no way will build genomes up -- which is what evos need to explain common descent.

[snorkild]

only weakly correlated =/= uncoupled

[SAWells]

In this week's Science, a neat experiment on yeast, where knockout strains were exposed to a wide range of small molecules, showed that 97% of the genes tested displayed a phenotypic effect.

[supersport]

In this week's Science, a neat experiment on yeast, where knockout strains were exposed to a wide range of small molecules, showed that 97% of the genes tested displayed a phenotypic effect.

mutations, in some situations can have phenotypic effects, but the problem is they can't add new structures. There's no doubt that knocking a gene out can deform or remove pieces of anatomy. The question is how animals get built up and where the information came from to do so.

[SAWells]

In this week's Science, a neat experiment on yeast, where knockout strains were exposed to a wide range of small molecules, showed that 97% of the genes tested displayed a phenotypic effect.

mutations, in some situations can have phenotypic effects, but the problem is they can't add new structures.

Wrong. You're still stuck in your "what's the single gene responsible for an entire organ?" misconception.

[Calilasseia]

Double Tail mutation in Betta splendens, anyone? :)