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Author Topic:   Criticizing neo-Darwinism
Adminnemooseus
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Message 256 of 309 (463681)
04-19-2008 1:04 AM
Reply to: Message 253 by randman
04-18-2008 11:13 PM


Randman's reluctance to supply a link
Not grabbing at anything. You know full well what the study is so don't make false accusations.....the simple truth is this site is censored according to the perception of the owner.

So cut the crap. If you have some integrity, link the paper and discuss the findings. If not, don't hide behind false accusations of hiding behind anything. you know full well I cannot link the study without being banned and may well be banned for merely mentioning it, despite it being a peer-reviewed paper by evos.

My "bolding".

I think the above is absolute nonsense. But if you truly think that link is so dangerous to you membership, how about e-mailing it to me? I'll take a look at it, and probably post it for you. Or I will tell you and all why the link can't be posted.

Please include a link to this message in any e-mail. Otherwise I might have problems tracking what the e-mail is relevant to.

No replies to this message by anyone, other than via e-mail.

Adminnemooseus


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randman 
Suspended Member (Idle past 3184 days)
Posts: 6367
Joined: 05-26-2005


Message 257 of 309 (463682)
04-19-2008 1:11 AM
Reply to: Message 256 by Adminnemooseus
04-19-2008 1:04 AM


Re: Randman's reluctance to supply a link
I thought you participated in the "discussion" of this link but maybe it was just percy and someone else. Here is the link per your request (though not in email form).

EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates

Percy's comments in admin mode suggest to me that linking this paper would not be acceptable to him. I would expect some here though to be familiar with the evidence mentioned, as on another thread there was an unchallenged comment:

the complexity of the rest of the animal kingdom being assumed to be due to the complexity of the common ancestor.

To be honest, it's not clear to me why the findings of this paper were deemed off-limits for it's own thread. Percy insisted I was misinterpreting it, but most of what I brought up was just quoting the paper itself.

My hope was that there would be sufficient familiarity with the evidence in this paper and elsewhere to bring up the facts relative to this thread without providing the link. It seems clear to me that the findings of this paper and elsewhere are relevant to genetic evolution.

Edited by randman, : No reason given.

Edited by randman, : No reason given.

Edited by randman, : No reason given.


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randman 
Suspended Member (Idle past 3184 days)
Posts: 6367
Joined: 05-26-2005


Message 258 of 309 (463685)
04-19-2008 1:40 AM


this may be of interest...
An important general implication that flows from these data is that gene loss may occur stochastically. If the genes in a pathway function only in that pathway, then one might expect that entire pathways would disappear following loss of one key component. However, the Hydra data appear to contradict this; most of the intracellular intermediates of Toll/TLR signaling are present despite loss of all of the major receptor types (both Toll/TLR and the IL-1R types known from more basal cnidarians are apparently absent from Hydra). Moreover, simple comparisons between related animals (for example, Nematostella versus Acropora) are unlikely to be informative in terms of understanding the origins of genes [50] - loss of a gene from Nematostella and loss of a specific function in the indirect developing urchin seems more likely than the independent co-option of the same protein to related roles in Acropora and a direct developing urchin. Stochastic loss underlying the distribution patterns of genes across the Metazoa may account for some cases of assumed lateral gene transfer - chance retention of an ancestral gene in one or a few animal lineages might easily be confused with lateral transfer.

http://genomebiology.com/2007/8/4/R59

It's worth noting the comment that "chance retention of an ancestral gene in one or a few animal lineages might easily be confused with lateral transfer." As to how this relates to NWR's theory of pseudogenes evolving without natural selection and then parts becoming coding genes for specific functions is that his idea, while not agreeing with it, at least holds out some promise of genetic complexity building up without morphological complexity so that from a position of massive genetic complexity, many animal lineages could evolve via LOSS of genes.

Keep in mind I am not arguing he is correct, but I do think some answer besides traditional NeoDarwinism of a gradual evolution of genes via random mutation and natural selection is necessary and am glad to see nwr moving away from the NeoDarwinian paradigm.

This article discusses these sorts of findings and proposes an alternative to NeoDarwinism for gene evolution.

http://www.machanaim.org/philosof/nauka-rel/universal_genome.htm

Edited by randman, : No reason given.


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Admin
Director
Posts: 12630
From: EvC Forum
Joined: 06-14-2002


Message 259 of 309 (463706)
04-19-2008 7:51 AM
Reply to: Message 253 by randman
04-18-2008 11:13 PM


Re: Back to basics
randman writes:

Not grabbing at anything. You know full well what the study is so don't make false accusations.....the simple truth is this site is censored according to the perception of the owner.

The place for these kinds of complaints, as I've told you many, many times, is Windsor castle. I had decided to ignore your statement that molbiogirl picked up on, and now you leave me no choice. Four days this time.

AbE:

So cut the crap. If you have some integrity...

Also, you must stop making the debate personal. Evidence, argument, rebuttal, evidence, argument, rebuttal, over and over and over again, that's all that is wanted here.

Please, no replies.

Edited by Admin, : Add another Forum Guidelines violation item.

Edited by Admin, : Add "no replies" comment.


--Percy
EvC Forum Director

This message is a reply to:
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Admin
Director
Posts: 12630
From: EvC Forum
Joined: 06-14-2002


Message 260 of 309 (463707)
04-19-2008 8:03 AM
Reply to: Message 254 by randman
04-18-2008 11:16 PM


Re: Back to basics
randman writes:

The data is there and you can find it quite easily.....you can even find where I've discussed it here at EvC or just do some googling.

I know I'm just wasting my breath, but at EvC Forum members are encouraged to make their arguments in their own words and support them with evidence. Telling people to go find the evidence to support your arguments by Googling is not permitted.

I'm going to begin operating on the assumption that, even though you keep returning after each suspension, that your goal is less constructive discussion and more getting a few rule-breaking shots in before being suspended again, so I'm going be more strict with you from now on. Anything in messages from you that doesn't directly and obviously address the topic will result in an immediate suspension, five days next time.

Please, no replies.


--Percy
EvC Forum Director

This message is a reply to:
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Percy
Member
Posts: 18871
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


Message 261 of 309 (463708)
04-19-2008 8:06 AM
Reply to: Message 255 by randman
04-18-2008 11:18 PM


Re: Back to basics
It doesn't look like this is leading toward a clarification of what you meant, so I guess we may as well just drop it. Perhaps it will come up again during the discussion.

--Percy


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Admin
Director
Posts: 12630
From: EvC Forum
Joined: 06-14-2002


Message 262 of 309 (463711)
04-19-2008 8:41 AM
Reply to: Message 257 by randman
04-19-2008 1:11 AM


Re: Randman's reluctance to supply a link
randman writes:

I thought you participated in the "discussion" of this link but maybe it was just percy and someone else. Here is the link per your request (though not in email form).

EST Analysis of the Cnidarian Acropora millepora Reveals Extensive Gene Loss and Rapid Sequence Divergence in the Model Invertebrates

Percy's comments in admin mode suggest to me that linking this paper would not be acceptable to him.

Randman is referring to his Acropora millepora and it's human genes thread proposal. Everyone is welcome to read that thread to see that Randman is incorrect to claim that my "comments in admin mode suggest...that linking this paper would not be acceptable..." I never made any such suggestion.

No link has ever been ruled off limits at EvC Forum.

No suggestion has ever been made that the link would not be permitted in this thread.

Randman is also clearly in violation of the Forum Guidelines to complain here about a thread proposal. As was clearly suggested at the end of that proposal, he should post to Topic Proposal Issues if he would like to reopen it.

And responding specifically to this:

randman writes:

To be honest, it's not clear to me why the findings of this paper were deemed off-limits for it's own thread.

The paper was not deemed off-limits. It was pointed out to Randman by both myself and AdminNosy that the paper did not support his argument, and that he was making an incorrect interpretation. I informed Randman that the thread would not be promoted as long as it contained references incongruent with his claims, because that would just result in a thread that would end up discussing not the topic but Randman's misinterpretation of the paper. Randman has made quirky misinterpretations of papers and scientists many times, and he always argues at length for them, and I informed Randman that EvC Forum would not be hosting these kinds of discussions anymore.

In sum, I'm very disappointed that Randman is apparently returning here after suspensions simply to be as difficult as possible. He is welcome to advocate any position he wishes as long as his conduct conforms to the Forum Guidelines. No one has ever been suspended at EvC Forum for their position.

Please, no replies.


--Percy
EvC Forum Director

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Wounded King
Member (Idle past 2379 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 263 of 309 (463727)
04-19-2008 12:36 PM
Reply to: Message 258 by randman
04-19-2008 1:40 AM


A general response
Hi Randman,

I'll try and address points from a number of your posts.

Message 242
Of course, but I can't tell you how often when someone not an evo points this out, someone from your camp drones on how this isn't the case

Well this seems very bizarre to me, I can't recall having seen this happening on this forum but I'll take your word for it.

In this manner then, genetic evolution proceeds alongside of morphologocal evolution.

Yes, but there is not a 1 to 1 linear correspondence. Morphological evolution certainly depends on genetic evolution but there can be a large amount of genetic evolution independent of morphology per se, i.e. evolution of genes involved with cellular metabolism and biochemistry or even elements of the immune system.

However, the problem with this story is it doesn't fit the facts. We see massive genetic complexity in very simple organisms with genes and genetic sequences for complex functions the simple organisms don't have.

I disagree and you would have to present substantial evidence to support this claim. Complex genetics in morphologically simple organisms is not sufficient as thee are other levels of complexity which may necessitate it, such as the metabolic or biochemical complexity I mentioned previously.

I'm assuming that the sort of thing you are talking about in terms of 'simple organisms with genes and genetic sequences for for complex functions the simple organisms don't have' you are thinking of things like homologues of the pax genes involved in eye development being expressed in sponges or various elements of the developmental gene network associated with the eye being found in 'primitive' organisms such as the platyhelminthes. I don't know of any examples of this sort of thing that would support your contention however.

Message 247
So you would think that we would see genetic expressions arise at the same time when the morphological traits arise. We should see genetic sequences for complex nerve function arise, for example, when complex nerve function was evolving.

This is true to some extent, but we would also expect these genetic traits to be principally based upon already extant genetic material. We would expect genetic networks related to complex nerve function to be highly integrated and derived from any simpler network involved in the development of simpler nerve function. I'll revisit this in the context of the paper you reference about A. millipora. Percy was quite right not to promote a thread whose very title 'Acropora millepora and it's human genes' conveys a gross misrepresentation of the papers results, one you persist with in your frequent references to 'human gene sequences' and 'human genetic expressions'. The genes were present in humans and A. millipora and not in Drosophila or C. elegans. That doesn't make them 'human genetic sequences'.

The fact that a species carries genes related to the those involved in the development of the nervous system does not imply we should expect to see something resembling the human nervous system in the organism. your argument relies heavily on the idea that these genes have no other conceivable function, this is easily shown to be false simply doing a literature search on the gene that the paper identifies as 'bilaterian genes whose specialized functions are associated with highly differentiated nervous systems' but which are not know to be present in any invertebrates. Of the three genes so identified 2 of them, Tumorhead and Churchill, are also involved in early morphogenetic movement in the developing embryo even in the first few cleavage stages in the case of Churchill in Zebrafish (Londin et al., 2007). Tumorhead has been shown to be similarly expressed at early stages in Xenopus (Traverso et al., 2006). Did you notice that neither of those species were human and yet had the genes you have been passing off as 'human gene sequences' in A. millipora.

As we gain more and more knowledge about the genomes of various species our understanding improves. In the absence of contrary evidence it was the most parsimonious interpretation to assume that genes only found in the vertebrate lineage evolved in that lineage after it diverged from the invertebrates. The data you refer to show this was not true in several cases and in those case the most parsimonious explanation becomes that they have been lost at some point in the evolutionary lineages of Drosophila and C. elegans.

Modern evolutionary biology has no problem with genetic loss, it is just another form of mutation. Whether such loss is actively adaptive in some way or simply serves to alleviate some burden on the cell is a moot point. Did the Drosophila lineage lose certain genes and concomitantly lose some morphological feature or did those genes simply become redundant for some reason and get discarded as excess baggage? It is an interesting question and not one really susceptible to an answer until we have wider body of genomic information to draw on.

Is our understanding of the evolution of life on earth being altered by this kind of research, yes it is. Is our understanding of the processes of evolution? Not so much. This doesn't require any rethinking of the mechanisms of random mutation and natural selection as the primary ones in adaptive evolution. It implies that the common ancestor of invertebrates and vertebrates is more complex than simply being the overlapping set of their gene complements but I see little if any support for your contention that...

the most primitive metazoan (the theoritical common metazoan ancestor) is thought to be incredibly complex genetically, perhaps as much as human beings.

... viewed even in the best possible light this is still pure hyperbole.

I look forward to your response when you can post again.

TTFN,

WK


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bertvan
Junior Member (Idle past 4104 days)
Posts: 29
From: Palm Springs California
Joined: 09-10-2007


Message 264 of 309 (463857)
04-21-2008 2:01 PM
Reply to: Message 263 by Wounded King
04-19-2008 12:36 PM


Re: A general response
NeoDarwinism argues that biological innovation “just happens, accidentally, for no particular reason”. Then, according to NeoDarwinism, the only known materialistic theory of evolution, “natural selection” somehow turns a collection of these random genetic accidents into biological adaptations. However, no one has come up with even a hint at how natural selection might accomplish such a feat.

Intelligent design proposes that intelligence exists as an aspect of reality. We know humans have the ability to make reasoned, purposeful choices. The same ability to a more limited degree can be deduced in animals. Even single cultured cells display an ability to make simple choices. Swarm intelligence has been observed. Intelligent Design argues that living organisms adapt responsively, intelligently and purposefully. Random accidents in their genomes are defects, some of which are corrected by purposeful genomic mechanisms, but none turn into biological features.

As an agnostic, I don’t speculate about the origin of an organizing intelligence of nature, any more than I speculate about the origin of matter and energy. Only atheists fear the recognition of intelligence as an organizing force of living systems, because they cannot deny the possible involvement of some god in a non material process such as intelligent organization.

Questions about Materialism
http://30145.myauthorsite.com/


http://30145.myauthorsite.com/

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Percy
Member
Posts: 18871
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.4


Message 265 of 309 (463865)
04-21-2008 3:14 PM
Reply to: Message 264 by bertvan
04-21-2008 2:01 PM


Re: A general response
Responding to the last paragraph first:

bertvan writes:

As an agnostic, I don’t speculate about the origin of an organizing intelligence of nature, any more than I speculate about the origin of matter and energy. Only atheists fear the recognition of intelligence as an organizing force of living systems, because they cannot deny the possible involvement of some god in a non material process such as intelligent organization.

I'm a theist, which for this thread, a science thread, is just as irrelevant as that you're an agnostic or that someone else is an atheist. The topic is neo-Darwinism, not theology.

NeoDarwinism argues that biological innovation “just happens, accidentally, for no particular reason”. Then, according to NeoDarwinism, the only known materialistic theory of evolution, “natural selection” somehow turns a collection of these random genetic accidents into biological adaptations. However, no one has come up with even a hint at how natural selection might accomplish such a feat.

All this proves is that *you* personally don't understand how mutation and natural selection work.

Intelligent design proposes that intelligence exists as an aspect of reality. We know humans have the ability to make reasoned, purposeful choices. The same ability to a more limited degree can be deduced in animals. Even single cultured cells display an ability to make simple choices. Swarm intelligence has been observed. Intelligent Design argues that living organisms adapt responsively, intelligently and purposefully. Random accidents in their genomes are defects, some of which are corrected by purposeful genomic mechanisms, but none turn into biological features.

Ignoring the errors (for example, "random accidents in their genomes" turn into "biological features" all the time, a famous example being Down Syndrome), to make a scientific claim you need an observable mechanism by which your intelligence operates.

--Percy


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teen4christ
Member (Idle past 4084 days)
Posts: 238
Joined: 01-15-2008


Message 266 of 309 (463866)
04-21-2008 3:14 PM
Reply to: Message 264 by bertvan
04-21-2008 2:01 PM


Re: A general response
bertvan writes
quote:
NeoDarwinism argues that biological innovation “just happens, accidentally, for no particular reason”. Then, according to NeoDarwinism, the only known materialistic theory of evolution, “natural selection” somehow turns a collection of these random genetic accidents into biological adaptations. However, no one has come up with even a hint at how natural selection might accomplish such a feat.

Does agnosticism also tells you to use a strawman argument against natural selection?

quote:
Intelligent design proposes that intelligence exists as an aspect of reality. We know humans have the ability to make reasoned, purposeful choices. The same ability to a more limited degree can be deduced in animals. Even single cultured cells display an ability to make simple choices. Swarm intelligence has been observed. Intelligent Design argues that living organisms adapt responsively, intelligently and purposefully. Random accidents in their genomes are defects, some of which are corrected by purposeful genomic mechanisms, but none turn into biological features.

As an agnostic, I don’t speculate about the origin of an organizing intelligence of nature, any more than I speculate about the origin of matter and energy. Only atheists fear the recognition of intelligence as an organizing force of living systems, because they cannot deny the possible involvement of some god in a non material process such as intelligent organization.



This is little better, if better at all, than "goddidit." It's an intellectual dead-end.

By the way, using strawman against an argument will never get you very far.


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teen4christ
Member (Idle past 4084 days)
Posts: 238
Joined: 01-15-2008


Message 267 of 309 (463867)
04-21-2008 3:15 PM
Reply to: Message 265 by Percy
04-21-2008 3:14 PM


Re: A general response
Percy writse
quote:
Ignoring the errors (for example, "random accidents in their genomes" turn into "biological features" all the time, a famous example being Down Syndrome), to make a scientific claim you need an observable mechanism by which your intelligence operates.

Forget down syndrome. Think sickle cell.

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bertvan
Junior Member (Idle past 4104 days)
Posts: 29
From: Palm Springs California
Joined: 09-10-2007


Message 268 of 309 (463885)
04-21-2008 5:41 PM


I was under the impreswsion that both Down's syndrome and sycle cell were defects. Firthermore, if genetic accidents, somehow turned into biological features by "natural selection" is a strawman, all you have to do is explain the real origin of biological features according to NeoDarwinism.

Edited by bertvan, : to add sycle cell


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Wounded King
Member (Idle past 2379 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 269 of 309 (463889)
04-21-2008 6:12 PM
Reply to: Message 268 by bertvan
04-21-2008 5:41 PM


The point is that any mutation, or 'genetic accident' if you insist, which isn't functionally neutral will produce a biological feature, i.e. a change in the observed phenotype of the organism. Most of these changes will themselves be effectively neutral, the majority of the rest will be detrimental and a slim few may be beneficial to the organisms reproductive success. It is the variation in these phenotypic traits that allows natural selection to occur as mutations increasing reproductive success will tend to be favoured.

To make your question work the way you seem to intend I think you need to expand upon what you mean by a 'biological feature', i.e. perhaps a complex feature of multiple independent parts.

TTFN,

WK


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Rahvin
Member
Posts: 3964
Joined: 07-01-2005


Message 270 of 309 (463890)
04-21-2008 6:21 PM
Reply to: Message 268 by bertvan
04-21-2008 5:41 PM


I was under the impreswsion that both Down's syndrome and sycle cell were defects. Firthermore, if genetic accidents, somehow turned into biological features by "natural selection" is a strawman, all you have to do is explain the real origin of biological features according to NeoDarwinism.

Your impression was (slightly) incorrect.

Biological features are not inherently positive or negative. That's a subjective judgment that can change depending on the environment.

sickle cell is the perfect example; while it causes problems, it does prevent malaria. If you're in an area rife with malaria-carrion mosquitoes, sickle-cell is a positive feature. If you're in an area where malaria basically does not exist, sickle-cell would be a negative feature.

You could make the same judgment with animal camouflage. A leopard blends into its normal environment, so its fur patterns are considered a "positive" feature. But if you put the leopard in a completely different environment like, say, a rain forest or a city street, it would stand out like a sore thumb.

Natural selection does not "turn" a genetic "accident" into a feature. Genetic "accidents" simply happen, and are the direct cause of any given feature. Natural selection determines whether any given feature is passed onto the next generation, but has nothing to do with the expression of a genetic trait - the genetic change is the cause of a change in a feature, all by itself. Multiple successive mutations passed on will build on each other to make more and more meaningful changes over time. This means that while individual mutations are relatively slight and sometimes have no real observable effect, over many successive generations those changes can build into something very observable, like a change in camouflage patterns.

Natural selection is an incredibly easy idea to grasp, so I'm surprised at how many people fail to do so. Natural selection is a blind process by which features that help an organism survive to reproduce will gradually become more prevalent in a given population compared to features that do nothing or actually hinder the organism's survival. This determination is not intelligent, but is rather wholly subjective dependent on the organism's environment, and a change in that environment can make formerly "negative" features into helpful ones and vice versa.

The Peppered Moth is another good example of this in action.

The moth originally had a light background with dark speckles camouflage pattern to blend in with the trees it tended to land on. Over a few generations, the British population of these moths actually changed colors - the soot from the Industrial Revolution was so thick that it darkened most surfaces including trees, and so the moths former camouflage suddenly made then stand out. The moths with mutations that made them darker were suddenly harder for predators to find, and over just a few generations the camouflage pattern of the entire population changed to one that is almost uniformly darkened.

Even more interesting is that, as environmental laws cleaned up British industry and the soot began to disappear, the moths have begun to change back to something like their original color patterns!

It's literally an observed case of natural selection guiding random mutation.

So again - you were incorrect to say that natural selection turns genetic accidents into features. Genetic accidents (mutations) are the cause of features themselves. Literally changing a gene (or several, as most features are not determined by a single gene in their entirety) will change a feature in the organism regardless of whether that organism survives or not. Natural selection is what we call the process by which those features are either encouraged or discouraged by environmental pressures like predators or food availability. Mutations cause the new or altered features, and natural selection causes those features to become more or less common in the population as a whole. The changes in frequency of given features in a population is evolution.


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