Moving from suspicion to evidence for ID

Just continuing from the last post:So could horizontal gene transfer (HGT), most likely viral in nature, be considered a possible mechanism/test for intelligent design? Before everyone blows up, I know its a weak test, but just for the fun of it what would the criteria be? Off the top of my head:1. Insertional specificity: HGT results in specific site insertion into the genome, not random. A majority of genes are found in specific areas of the genome in relation to other genes.2. Heretibility: HGT must result in germ cell insertion, must be heritible.3. Species specific: Wouldn't make much sense to give numerous species increased brain capacity, for example.4. Non-virulent infection: Actually, now that I think about it, HGT conferred survival would be a great way to select for insertional mutants, causing the non-insertional mutants to die off. Harsh, I know.I'm not an expert in the field of viral vectors, maybe someone who is could comment. However, the real problem would be determining the origin of the vector. Humans have a long history of anthropomorphizing nature, giving inanimate or non-conscious things human attributes and intentions. Even if these criteria were met, it still probably wouldn't rule out a natural origin.[This message has been edited by Loudmouth, 08-12-2003]

Hi Loudmouth,1. The problem with this is that retroviral integration is often in specific regions of the genome but it is a constraint of retroviral reverse transcription and integration possiblities rather than an example of design. Strand breaks are often required for integration and those will likely be in regions that are transcriptionally active so it is no wonder that the elements accumulate in regions where genes are transcribed. In addition, many retroelements have LTRs and end up integrating by homologous recombination with LTRs already present. The system is random but integration sites are not equiprobable...however, there are completely natural (and fairly well researched) explanations that don't require intelligence...though I will point out, a lot of HGT is not viral in nature.2. This does not argue for design...natural evolution requires heritablility..design does not.3. The problem here is that HGT will originally be a discreet event and so like every germline mutation, it will be species specific. The Wollbachia genome integration is specific to one species of beetle that for the life of me I cannot remember the name of right now..embarrassing since I recently prepared a journal club lecture on this HGT example 4. I am not sure how virulence would be important for a design argument. Presumably the better "designed" organism would become predominant but would not require the killing off of the less well designed form.Viral vectors are a pain...they have the nasty tendency of kicking out the genes you want expressed and re-froming wildtype virus...they also like to recombine with endogenous viruses...As Mr. Hambre pointed out..I am acting as resident ID critic without actually contributing to the topic of the thread...try as I might I cannot think of evidence that would support ID...I will try to post something later that you guys can rip apart rather than me being in the easier and more comfortable position of ripping on other peoples ideas cheers,
M

To Mammuthus,I can't think of any reason to support ID either, mainly because every argument made for it can be as easily explained by evolution through natural selection which can actually be observed.That being said, it still behooves us as evolutionists to state what we would expect to see if intelligent design was wholly or partially responsible for species diversity (kind of a null hypothesis).It sounds like you've done lab work or at least are familiar with experimental design. In you're opinion (as the self proclaimed thread expert), if there were any indication of ID in the mechanisms of HGT, what would you look for. Or better yet, what type of HGT event would stand out from what you would consider a natural event.Just for example, if our lab received a antibiotic resistant strain of streptococcus and we were able to isolate the gene/s involved in conferring resistance we would not expect them to be surrounded by multiple cloning sites or E. coli ori sequences. This would be more indicative of a "man made" strain versus a naturally occuring one.Curious Evolutionist,Loudmouth[This message has been edited by Loudmouth, 08-13-2003]

Hi Loudmouth

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That being said, it still behooves us as evolutionists to state what we would expect to see if intelligent design was wholly or partially responsible for species diversity (kind of a null hypothesis).

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I agree. I wish the ID proponents actually thought this as well...but for the most part all I have heard from their camp is "evidence for ID is self evident"..or "a flagella could not evolve".

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It sounds like you've done lab work or at least are familiar with experimental design. In you're opinion (as the self proclaimed thread expert), if there were any indication of ID in the mechanisms of HGT, what would you look for. Or better yet, what type of HGT event would stand out from what you would consider a natural event.

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I hope I did not proclaim myself an expert somewhere , that would be a sure indication that I am suffering from early senility.
I have a Ph.D. in human genetics but have worked on the phylogeny and potential causes of extinction of Pleistocene megafauna for several years. I now work on prions and endogneous retroviruses to pay the rent. I don't consider myself an expert..just a scientist who can't focus I think one example of a potential support for ID would be if Lamarkian evolution had been correct. If one could observe species massively changing phenotype to adapt to a trait within their own lifetime and then passing the trait on that would be a problem for random mutation and natural selection (it would also screw genetics).

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Just for example, if our lab received a antibiotic resistant strain of streptococcus and we were able to isolate the gene/s involved in conferring resistance we would not expect them to be surrounded by multiple cloning sites or E. coli ori sequences. This would be more indicative of a "man made" strain versus a naturally occuring one.

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This is a good point. We actually can identify organisms that have been modified genetically i.e. intelligently by humans as opposed to naturally occuring organisms (the people who think the government created HIV to kill off minorities not withstanding)...if we found DNA from neandertals that had multiple cloning sites, pUC vector sequences, the genes for GFP inserted with a CMV promoter in a specific part of the genome etc., viral promoters expressing genes for malarial resistance, whatever, it would certainly be odd and would certainly suggest that somoene had tinkered with the genome of this group. On the other hand, is this the best evidence one can come up with for ID...i.e. I will believe it as I wait for that result to show up?..this is not much different than believing in the tooth fairy.But the line of reasoning you bring up is a good one, why is it we can identify bacterial, plant, and animal sequences that have been modified genetically by humans yet find no such obvious evidence otherwise for such intervention in natural systems if ID is self evident?cheers,
M

I'd have thought that the obvious answer to that would simply be that we don't know what to look for. The Intelligent designer obviously has a more elegant way of fiddling with genetics and doesn't need to leave multiple cloning sites laying around. All this line of argument shows is that whatever the mechanism is it isn't one a modern molecular geneticist uses or recognises.

Hi WK,
That we are failing miserably to even come up with anything that would suggest ID is fairly telling...everything can be batted down as incorrect or has a testable natural explanation...or is an argument from incredulity...you have anything that would suggest ID as opposed to natural mechanisms?cheers,
M

Nothing that actually exists I'd go with Holmes suggestion that if there were widespread evidence of specific 'pre-adaptation'it might be compelling evidence. At the moment there isn't even anything suggestive let alone compelling.

Even worse, the evidence is against pre-adaptation so on top of having to find widespread evidence, they would have to explain away the counter evidence.

Just like mammuthus said. Even if that criteria were enough to suggest ID as a valid theory, and enough accumulated evidence along that line MIGHT start challenging evolution as the SOLE cause of change... there simply is no such evidence like this.On top of that, all the evidence we do have suggests the complete opposite. So while the criteria may be nice to have in one's backpocket (along with theories of how big the universe is) one can't hold out for that evidence to start accumulating.Evolution is the best and at this point the only suggested mechanism for speciation. ID has nothing.------------------
holmes

Maybe I'm missing something (wouldn't be the first time)
but doesn't evolution rely on pre-adaptation (sort of).That is, the variant has to be present to exploit the change
that makes its variation beneficial.If there are four individuals in a population of 40,000 that
have an adaptation that helps them survive an asteroid impact
(like, for example, a force-field ) then after the event
that's whats left and hey-presto hundreds of 'em pop-up
and so suddenly appear in the fossil record.The chances of individuals appearing in the fossil record must
be related to the number of that type of individual.So a sudden change like that in the fossil record wouldn't
indicate intelligent design at all.

Because of replication errors etc. there exists variation in every population. This is not pre-adaptive. In the cases where the environment changes such that none of the existing variants in the population can survive you get extinction i.e. my namesake. More often, the changes are less catastrophic such that some variant has a slight edge (or in some instances a dramatic advantage over the others)...but this is hardly a pre-adaptation...a slightly deleterious mutation that becomes an advantage due to a shifting environment is hardly evidence of design..that is more like hindsight is 20/20 thinking i.e. I knew that mutation would be the advantagous one after the fact.

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that is more like hindsight is 20/20 thinking i.e. I knew that mutation would be the advantagous one after the fact.

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That's more or less what I meant -- in hindsight evolution
operates in a pre-adapted way (it's why I said 'sort of').The adaptation that prooves advantageous pre-existed.It means that even if you find an entire population
that had an adaptation that would be beneficial in a subsequent
environment it would NOT be evidence of intelligence ... it's
expected that such traits would exist.Apart from a code in the DNA that says 'made for the congo'
or somesuch I cannot think of anything historical that could
indicate intelligent intervention.If we found a living population that had some odd trait that
seemed at odds with their environment, and then their environment
suddenly changed to suit them, now THAT would be suspicious.I asked for an ID hypothesis (and didn't get one), but wonder
whether IDers claim that god (sorry the IDer {a rose by any
other name...}) intervenes along the way, or set
things in motion and let them run (kind of like a science
project).Each premise would presumably leave different signs (if any
signs could be left).

Sorry Peter,
I realized only after posting that I seem to be following you from thread to thread contradicting you. I should have stated that you have a good point. However, I would not argue that the survivors of a dramatic environmental shift necessarily are adapted to the environment. If they merely survive, even in low numbers whereas other variants do not then there is at least a population that has a chance to adapt to the environment. There are a lot of false starts in evolution that come and go..look at the Kakapo....

No problemo ... after-all if no-one disagreed with me
I'd get bored very quickly (and suspicious ).I wasn't really suggesting that the survivors necessarily
had an adaptation that aided their survival, only that
if they did this would appear, in hindsight, very much like
the suggestion for evidence of intelligent intervention.i.e. the suggested evidence is not sufficient.