Giardia lamblia, polyadenylation, and irreducible complexity

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(The following is a slight adaptation of this essay. Readers may post questions and/or comments there as well as here.) As this series of essays has explained, the polyadenylation of messenger RNAs is a vital aspect of gene expression in eukaryotic cells (and a not-so-unimportant facet of RNA metabolism in other contexts). Polyadenylation is mediated by a sizeable complex that includes various RNA-binding proteins, nucleases, and other interesting activities. Genetic studies in yeast indicate that virtually every subunit of the core complex is essential - for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo. (This review is freely available and serves as a good starting point for readers who wish to explore the subject further.) Biochemical and/or immunological depletion studies reveal a similar scenario in mammals, and a less-expansive set of studies suggests that a similar rule of thumb will apply in plants. The bottom line of all of this is that almost all of the subunits of the polyadenylation complex seem to be essential - remove one, and the complex cannot function. In the vernacular of a proponent of intelligent design, the polyadenylation complex would seem to be irreducibly complex.

It is in this context that the recently-completed genome of the parasitic organism Giardia lamblia enters the fray. Last year, the complete sequence of G. lamblia, some 12 million base pairs, was determined and analyzed. The authors of the study published in Science noted a number of interesting things - a preponderance of genes encoding protein kinases, evidence for substantial horizontal gene flow from bacteria and archaebacteria, and a streamlined core gene expression machinery (transcription and RNA processing). This streamlining is especially notable in the case of the polyadenylation machinery. Remarkably, of all the subunits in the yeast complex, genes for only three* can be found in G. lamblia (see the figure that follows this paragraph - adapted from Fig. 1 of Morrison et al.).

MorrisonFig1.jpg Naturally enough, one of these is the poly(A) polymerase (PAP). The other two polyadenylation-related proteins encoded by the G. lamblia genome correspond to Ysh1 and Yth1 (whose mammalian counterparts are CPSF73 and CPSF30, respective). Interestingly, as summarized here, these two subunits are the two to which nuclease activity has been ascribed. Also interestingly, the only RNA binding subunit amongst those seen is Yth1 (=CPSF30). Other subunits are missing. Thus, no other RNA binding subunits are apparent, none of the scaffolds (CPSF160/Yhh1, CstF77/Rna14, Fip1, symplekin/Pta1) are seen, and most of the subunits that have been shown to interact with the transcription complex (CPSF100/Ydh1, CstF50, and Pcf11, to name three) are absent. Indeed, entire complexes (CstF, CFmI, CFmII) appear to be missing.

What might these startling omissions mean? One possibility is that functional counterparts for most of these proteins exist, but that they have diverged so extensively as to be unrecognizable. This might be the case for some of the missing proteins, but many of these are so highly-conserved between plants and animals that this seems an unlikely explanation.

Another possibility is that mRNAs are in fact not polyadenylated in G. lamblia. This is apparently not the case, as cDNAs can be prepared using the usual methods (priming reverse transcription with oligo-dT). Moreover, these cDNAs have untemplated poly(A) tracts, and some limited sequence-gazing can identify a putative polyadenylation signal.

Neither of these possibilities seems likely. Which leaves us with the remarkable likelihood that mRNA polyadenylation in Giardia is mediated by a highly-reduced complex of but 3 proteins. This in turn brings us to some fascinating discussion, about both function and evolution.

First, about function. Absent some studies dedicated to polyadenylation mechanisms in Giardia, it’s hard to make sense of the absence of so many essential components of the polyadenylation apparatus. But the fact that the Giardia complex consists of the two known endonucleases is interesting, as it suggests that the very core of the complex in eukaryotes is an endonucleolytic one. It also suggests that, as we peer ever more closely into the complex in other organisms, these two subunits will attract more attention. Other questions about RNA recognition and of links with transcription and splicing also come to mind. For example, might the RNA-binding activity of Yth1/CPSF30 play a more prominent role in polyadenylation signal recognition than has been assumed? Is there an obligatory link between transcription and polyadenylation? If so, what is the link in Giardia, and what might this suspected mechanism tell us about the analogous link in other eukaryotes? Etc., etc., etc.

Which brings us to the evolution of the complex. Giardia has gained some notoriety of sorts, having been identified at times as a very primitive, pre-mitochondrial eukaryote, or as a still-primitive eukaryote that lost its mitochondria. These two scenarios regarding the mitochondria of Giardia give us a similar set of contrasting pathways regarding the evolution of the polyadenylation complex. One scenario would be that the Giardia polyadenylation complex resembles the primordial eukaryotic complex, that the first polyadenylation apparatus consisted of little more than a nuclease and a polymerase. The complex we seen in other eukaryotes would be derived from a series of co-options, recruitments, and duplication events, all building on this simple beginning. Of course, the most exciting aspect of this scenario is that it gives us a remarkably clear link to nucleolytic activities in bacteria; this follows from the structural and functional similarities between CPSF73/Ysh1 and RNAse J (noted here).

The alternative is that the Giardia complex has lost most of the subunits that we see in other organisms. This seems unlikely, given the essential nature of most of the subunits in yeast. However, some differences in this regard exist between yeast and other eukaryotes; thus, Yth1 is essential in yeast, but its Arabidopsis counterpart is dispensible for viability. In any case, this alternative would provide us with a clear example of how extensively an irreducibly complex mechanism can evolve.

Hopefully, this essay has taught readers a thing or two. More importantly, in the best of cases, it has raised a number of questions. There may be some answers, but for many of these there await much experimentation and exploration.

Morrison, H.G., McArthur, A.G., Gillin, F.D., Aley, S.B., Adam, R.D., Olsen, G.J., Best, A.A., Cande, W.Z., Chen, F., Cipriano, M.J., Davids, B.J., Dawson, S.C., Elmendorf, H.G., Hehl, A.B., Holder, M.E., Huse, S.M., Kim, U.U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J.E., Palm, D., Passamaneck, N.E., Prabhu, A., Reich, C.I., Reiner, D.S., Samuelson, J., Svard, S.G., Sogin, M.L. (2007). Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science, 317(5846), 1921-1926. DOI: 10.1126/science.1143837

* - in the figure from Morrison et al., Pab1, RNA polymerase II and Glc7 are also noted as polyadenylation factor subunits. Pab1 is one of two poly(A)-binding proteins that plays roles in polyadenylation in yeast; this protein, as well as the G. lamblia protein identified in this study, is distinct in sequence and domain composition from the nuclear poly(A) binding proteins seen in mammals and plant. RNAP II is so considered because it is a scaffold of sots, upon which numerous other polyadenylation factors assemble; this function is needed for efficient polyadenylation. Glc7 is a protein that consistently purifies with the yeast polyadenylation complex. As it is not considered historically to be a core polaydenylation complex subunit, I have not elaborated on it in this essay.

[updated on Aug 30 - Carl Zimmer noted, if more briefly, the curious reduction of the Giardia polyadenylation complex in this essay. I didn’t know of this until today, but thought it appropriate to mention.]

75 Comments

Wow. Impressive essay. I bewilders me that evolution can even track into the germs on everyday life. Bravo truly.

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

Laura said:

Wow. Impressive essay. I bewilders me that evolution can even track into the germs on everyday life. Bravo truly.

Giardia lamblia is also known as “hiker’s bane,” or “happy-faced bug,” due to it producing symptoms including painful diarrhea and nauseating gas, and because it looks like a cartoon face in the light microscope.

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

What sort of relationship? Binding legal contract, platonic?

Laura from the Genome Biology thread Wrote:

I have a few questions. I claim to be neither Evolutionist nor Christian, rather I would accept the title ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have.

Its not so much about the physical evidence, rather I have decided to go much deeper. I am confused on several subjects.

If there is a god, would you consider him unjust and unfair? Why or why not?

And,

Laura from this thread Wrote:

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

Assuming “Laura” is sincere for the moment; I would suggest that there are many books out there that cover this area.

Before we get off on unnecessary tangents, we should ask which ones has he already read?

Dear Mike,

Thanks for questioning “Laura”:

Mike Elzinga said:

Laura from the Genome Biology thread Wrote:

I have a few questions. I claim to be neither Evolutionist nor Christian, rather I would accept the title ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have.

Its not so much about the physical evidence, rather I have decided to go much deeper. I am confused on several subjects.

If there is a god, would you consider him unjust and unfair? Why or why not?

And,

Laura from this thread Wrote:

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

Assuming “Laura” is sincere for the moment; I would suggest that there are many books out there that cover this area.

Before we get off on unnecessary tangents, we should ask which ones has he already read?

Laura could start by reading either of Ken Miller’s books, especially “Finding Darwin’s God”.

Appreciatively yours,

John

Dear Arthur,

This is absolutely brilliant. It is analogous to what I have seen Ken Miller describe with regards to just how “irreducibly complex” the bacterial flagellum is. Am looking forward to reading your future posts.

Regards,

John

P. S. Any chance of sending this to Ken? I think he’d be interested. You can tell him that I had suggested it.

Laura from this thread Wrote:

I have a few questions. I claim to be neither Evolutionist nor Christian, rather I would accept the title ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have.

Its not so much about the physical evidence, rather I have decided to go much deeper. I am confused on several subjects.

If there is a god, would you consider him unjust and unfair? Why or why not?

And,

Laura from the Giardia Lamblia thread Wrote:

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

Assuming “Laura” is sincere for the moment; I suggest that there are many books out there that cover this area.

Before we get off on unnecessary tangents, we should ask which ones has he already read?

Oops! Sorry about that last post. It was supposed to go to the Genome Biology thread to alert them there also. I had the wrong screen up.

Well once again, this proves that the concept of irreducible complexity is merely the product of a distinct lack of imagination. On the other hand, it beautifully confirms yet another prediction of what we would expect to see if the theory of evolution is true.

The most interesting issue to me is the phylogenetic position of Giardia. Is it basal in the eukaryote, thus representing an intermediate form between between prokaryote and eukaryote polyadenylation systems, or is it a degenerate eukaryote that branched off after mitochondria were acquired and subsequently lost both mitochondria and most polyadenylation genes? Quite likely, ribosomal sequences will yield the best answer to this question. It seems that the hypothesis that this represents an intermediate form would be the most parsimonous explanation.

Of course, this is also an example of the great predictive power of evolutionary thoery and the great value of comparative genomic data.

A slight correction:

Giardia has gained some notoriety of sorts, having been identified at times as a very primitive, pre-mitochondrial eukaryote, or as a still-primitive eukaryote that lost its mitochondria.

It has been proven pretty conclusively that neither Giardia nor any other known eukaryote is primitively amitochondriate. Furthermore, it has become apparent that there are no “primitive” eukaryotes (unless by “primitive” one means “unicellular”) – the phylogenies that placed Giardia as an early-branching (and thus primitive) organism have been shown to be fundamentally flawed.

It is not inaccurate to say that Giardia is a very highly-evolved organism in many ways, extremely specialised for its parasitic niche. The cell itself is quite highly organised. Of course, it retains a number of primitive features, and is secondarily simplified; the interest that came from its having been thought of as a primitive organism has not been misplaced. However, it is misleading to imply that such placement is still considered at all current.

An excellent and comparatively accessible review on this topic is Simpson, A. G. B.; Roger, A. J. (2004): “The Real ‘Kingdoms’ of Eukaryotes”. Current Biology 14 (17): R693-R696. [Full disclosure: one of the authors is my Ph.D. supervisor. He did not put me up to this – it really is a good paper.]

Oh, and the disease that it causes goes by other names as well, such as “backpacker’s diarrhoea” and my favourite, “beaver fever”.

Opisthokont [#1]

Sorry to waste the bandwidth, but the first page of the Current Biology paper is blank. I’m using Acrobat Reader 8 under OSX 10.5.4, and the alert message says the error is in the document.

The balance of the paper downloads fine.

I am not a software geek, so it could well be my fault and i don’t know enough to realize it.

fusilier James 2:24

Thanks to all for the commentary, and for the kind remarks and glowing reviews. If I may add a couple of brief comments:

John Kwok, I would expect that Ken Miller follows The Panda’s Thumb. If you (or anyone else reading this) wishes to send him a heads-up, feel free.

Opisthokont, your comment is most welcome. By “notoriety”, I hoped to convey that there has been considerable discussion about the place of Giardia on the tree of life. I have no wish to insinuate myself into this discussion, and I would hope that readers do not conclude from my essay that I am making any claims. For my purposes, the two possible extremes (deep-branching vs highly-reduced) are good contexts (pretexts?) for two contrasting pathways of origination of the polyadenylation complex in Giardia. Either pathway is fascinating, informative, and ultimately good fodder for a refutation of the ID use of irreducible complexity.

Opisthokont’s comments are well taken. Those of us who call ourselves protistologists are slowly coming to the realization that an extant example of the earliest eukaryotes is unlikely to be found. None the less we can gain a vision of what this progenitor of all nucleated organisms was like by studying “odd-ball” organisms such as Giardia, Reclinomonas, Retortamonas, etc.

Nothing fries my lunch more than when cell biologists examine a system in yeast, mammals, and maybe some invertebrate and conclude “Ah-ha! It is nearly identical in all three and therefore MUST be very ancient”

As “Opisthokont’s” name implies (brilliant choice by the way) the only thing it tells us is that yeast and animals belong to the same supergroup clade (Adl et al. 2005). Another example of our misguided animal-centric view of biology.

Stanton said:

Giardia lamblia is also known as “hiker’s bane,” or “happy-faced bug,” due to it producing symptoms including painful diarrhea and nauseating gas, and because it looks like a cartoon face in the light microscope.

Having had a bought with this bugger after insufficiently treating mountain stream water prior to ingesting it, there is nothing happy about it. Twenty one and in prime shape, I went from 155 pounds to 140 in a matter of days wherein I lived in the bathroom when I wasn’t crawling. The early stages at altitude were a joy beyond measure. Just don’t even think about it.

Laura has me cautiously optimistic. Ask away Laura.

Science Avenger Wrote:

Laura has me cautiously optimistic. Ask away Laura.

She needs to answer some questions on this and the other thread as well as ask the ones she alluded to yesterday. I too always give newcomers the benefit of the doubt at first, but sadly it has been unwarranted nearly every time.

Frank J said:

She needs to answer some questions on this and the other thread as well as ask the ones she alluded to yesterday. I too always give newcomers the benefit of the doubt at first, but sadly it has been unwarranted nearly every time.

I would suggest that this thread ignore the posting (or delete it as a duplicate) since it being addressed elsewhere … though so far the responses, which have been consistently on the theme of “WTF?”, have received no reply in return.

Giardia … oh yeah, those protozoans that look like stubby tadpoles with two eyelike suckers on the front. “Mother Nature rides a broomstick.”

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Opisthokont,

Thanks for the great reference. It would appear that Giardia has most likely sencondarily lost mitochondria, possibly due to the parasitic life style. It could still represent a basal eukaryote lineage and thus an intermediate in the evolution of euraryotic polyadenylation systems however.

Here is another reference on the phylogenetic position of Giardia:

BMC Evolutionary Biology 8:205 (2008) Available on Science Direct

Either way, Giardia once again demonstrates that irreducible complexity is not a valid concept. There are more ways to produce a complex system then are dreamt of by Behe.

Laura said:

Wow. Impressive essay. I bewilders me that evolution can even track into the germs on everyday life. Bravo truly.

But I do have a few questions. Not necessary on this essay but on evolution in general. They are quite simple really. I claim to be neither Evolutionist nor Christian, rather I would accept the statement ‘interested’. I am writing a paper on it’s relationship and I need someone to answer a few questions I have. You up for it mate?

Wild stab in the dark, but my bet is that Laura is at least a moderate case of some mental illness. I have had a few friends who were under psychological care (I never asked for a particular diagnosis) and they both had a tendency to use words in this somewhat … weired… fashion. Amusing enough to talk to, though.

“rather I would accept the statement ‘interested’?”

This does not seem to be the common mistake of a non-native speaker. Seriously, who talks like that?

Anywho, I can’t really see any constructive reason for responding to her particular question…

iml8 said:

Giardia … oh yeah, those protozoans that look like stubby tadpoles with two eyelike suckers on the front. “Mother Nature rides a broomstick.”

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Actually, Hiker’s bane only has one sucker: the pair of eyes are actually a pair of nuclei.

Dear Arthur,

Ken is probably busy preparing for the fall semester at Brown now, so there’s an excellent chance he’s missed it. His e-mail address is listed at www.millerandlevine.com, and you have my permission to mention me, as someone who suggested that you should contact him (I’ve known Ken for years. Back in the early 1980s I assisted him in his very first debate against a creationist which was held at Brown’s hockey rink.).

Regards,

John

Amongst us parasitologists Beaver Fever also goes by “The Explodo Sh-ts”… (While I’ve never experienced it myself I take it on good word that the fits very well…)

Please tell the McCain/Palin Campaign (preferrably politely) why teaching creationism in our public schools around America is superstitious and is not in our nation’s best interests. These are the feelers McCain has out there, the way in which Americans can have a voice and be heard by his campaign:

Contact his campaign directly here:

http://www.johnmccain.com/Contact/

Or go to his blogs and leave a polite message about the subject matter wherever appropriate:

http://www.johnmccain.com/blog/

Remember, McCain does a lot of things right and is a great heroic war veteran who genuinely puts his country first, but Creationism is one key area where he is completely wrong and could potentially create a major setback for American students and businesses. We can’t let America fall behind foriegn countries in the departments of Science and Technology because of his superstitious beliefs.

Dear quantum_flux,

Thanks, I strongly endorse your remarks, with special emphasis on politeness:

quantum_flux said:

Please tell the McCain/Palin Campaign (preferrably politely) why teaching creationism in our public schools around America is superstitious and is not in our nation’s best interests. These are the feelers McCain has out there, the way in which Americans can have a voice and be heard by his campaign:

Contact his campaign directly here:

http://www.johnmccain.com/Contact/

Or go to his blogs and leave a polite message about the subject matter wherever appropriate:

http://www.johnmccain.com/blog/

Remember, McCain does a lot of things right and is a great heroic war veteran who genuinely puts his country first, but Creationism is one key area where he is completely wrong and could potentially create a major setback for American students and businesses. We can’t let America fall behind foriegn countries in the departments of Science and Technology because of his superstitious beliefs.

Unlike Dubya, he is not a staunch Xian creo supporter. If I may, I would add that you might wish to echo Ken Miller’s concern - as noted in his recently published “Only A Theory: Evolution and the Battle of America’s Soul” - that we, the United States, are in danger of losing our scientific and technological superiority vis a vis the rest of the world if ID creationism and other forms of creationism are given political support as viable alternatives to evolution in science classrooms. Both Ken Miller and Niles Eldredge have emphasized the economic danger posed by creationism to America’s economic future in their recent books pertaining to creationism.

Appreciatively yours,

John

Thanks, QF. I will do that. And I would do it even if I were still a Democrat.

Tim Pawlenty went on the record this morning on Meet the Press as not understanding what actual education policy takes place in Minnesota. I don’t have a transcript, but I was watching when Brokaw pushed him on Palin’s support for Intelligent Design and he claimed that it was a local control issue in Minnesota which it is not. The state standards are pretty clear, and I am sure MNSCE supporters will kindly note how teaching creationism/ID has already been shown once in this state to be illegal.

Dear JGB,

That’s interesting:

JGB said:

Tim Pawlenty went on the record this morning on Meet the Press as not understanding what actual education policy takes place in Minnesota. I don’t have a transcript, but I was watching when Brokaw pushed him on Palin’s support for Intelligent Design and he claimed that it was a local control issue in Minnesota which it is not. The state standards are pretty clear, and I am sure MNSCE supporters will kindly note how teaching creationism/ID has already been shown once in this state to be illegal.

He may be trying to ignore it. On the other hand, I distinctly remembering Bobby Jindal pledging his support on “Face the Nation”, a few weeks before he signed the Louisiana Academic Freedom bill.

John

quantum_flux said: Please tell the McCain/Palin Campaign (preferrably politely) why teaching creationism in our public schools around America is superstitious and is not in our nation’s best interests. These are the feelers McCain has out there, the way in which Americans can have a voice and be heard by his campaign: Contact his campaign directly here: http://www.johnmccain.com/Contact/

The website barfed, so I emailed McCain. Here’s what I just sent:

Please do not let religious fanatics hijack science as has been done in the Bush administration.

Particularly, please understand that America’s standing in the world depends on strong support of science. The lies of some religious fanatics about the scientific fact of evolution - their refusal to let go of the superstition of creationism, “creation science” or intelligent design creationism - will cripple our country.

For the sake of our country’s future, you must take a stand for evolution and against creationism - even though this may alienate some of your base.

Essentially every actual science organization in the United States has issued a statement that evolution is a fact and that creationism, “creation science” and intelligent design creationism are not science but religion - and religion must not and cannot be taught as science in public schools.

Please take a strong stand on this.

mafarmerga said:

Nothing fries my lunch more than when cell biologists examine a system in yeast, mammals, and maybe some invertebrate and conclude “Ah-ha! It is nearly identical in all three and therefore MUST be very ancient”

As “Opisthokont’s” name implies (brilliant choice by the way) the only thing it tells us is that yeast and animals belong to the same supergroup clade (Adl et al. 2005). Another example of our misguided animal-centric view of biology.

Thanks all for the glimpses into interesting research. I can’t remember if it has been discussed here at Panda’s Thumb, but The Loom portrayed a large scale analysis of lateral transfer which illustrates (nice pictures, btw) some trends among the massive exchanges:

Analyzing this tree bush mangrove thicket Gordian knot, Dagan and her colleagues found a fascinating interplay between vertical and lateral gene transfer. If you look at any one of the 181 genomes, 81% on average of its genes experienced lateral gene transfer at some point in its history. So clearly lateral gene transfer is rampant. But once genes made the jump, they tended not to make another one–in fact, Dagan and her colleagues conclude that most became trapped in vertical descent. [Emphasis added.]

Btw, I’m curious why lateral transfers becomes trapped. A macroevolution mechanism?

PS. My proposal for embellishing “The Tree of Life” isn’t “The Gordian Knot of Life” or “The DAG (Directed Acyclic Graph) of Life” but “The Canopy of Life”, seeing those pictures.

Dear Paul,

As a McCain supporter I appreciate your remarks and am very, very glad that you e-mailed him (I’m working on a longer plea - but not too long - which I will send to him early this week.):

Paul Burnett said:

quantum_flux said: Please tell the McCain/Palin Campaign (preferrably politely) why teaching creationism in our public schools around America is superstitious and is not in our nation’s best interests. These are the feelers McCain has out there, the way in which Americans can have a voice and be heard by his campaign: Contact his campaign directly here: http://www.johnmccain.com/Contact/

The website barfed, so I emailed McCain. Here’s what I just sent:

Please do not let religious fanatics hijack science as has been done in the Bush administration.

Particularly, please understand that America’s standing in the world depends on strong support of science. The lies of some religious fanatics about the scientific fact of evolution - their refusal to let go of the superstition of creationism, “creation science” or intelligent design creationism - will cripple our country.

For the sake of our country’s future, you must take a stand for evolution and against creationism - even though this may alienate some of your base.

Essentially every actual science organization in the United States has issued a statement that evolution is a fact and that creationism, “creation science” and intelligent design creationism are not science but religion - and religion must not and cannot be taught as science in public schools.

Please take a strong stand on this.

Appreciatively yours,

John

McCain does a lot of things right and is a great heroic war veteran who genuinely puts his country first,

In the last presidential election, many who loudly proclaim the importance of military service voted against the war hero and for the two men who made a point of not going to Vietnam. One would think that after years of 5-13 discharges, outing CIA agents, and not giving GI’s personal armor, that vets would vote against the Republicans in mass.

I am sorry for getting political, the PT is not for that, but some things need a response. Pressuring McCain about ID is worth a try. Maybe constant pressure will keep Palin defensive.

Dear Frank,

I intend to remind McCain of the excellent research done by Arizona biologists at both the University of Arizona and Arizona State University. If you decide to “pressure” him about ID creationism, then please do so in a respectful, quite courteous, manner.

John

RWard said:

I think you need to have Mom wash out your mouth with soap. And what are these children being lied to about? Are you OK?

The lie is that the creationists/intelligent design proponents are posing valid criticisms of evolutionary theory. There are lots of debates in biology. Talk to your class about group selection or stochastic processes and the differing ideas biologists have about those ideas and I have no problem. Tell your class that ‘irreducible complexity’ poses a serious probhlem for evolutionary theory and you’re lying.

jobby said:

The lie is that the creationists/intelligent design proponents are posing valid criticisms of evolutionary theory.

… who determines what is a valid criticism??

The scientific community determines what is and what is not valid scientific criticism. Scientific criticism is intended to either improve or replace some aspect of a science. Given as how the alleged criticisms of both creationists and intelligent design proponents are based on a combination of ignorance, lies and a malicious need to spread misinformation, and given as how both creationists and intelligent design proponents have confessed to having absolutely no desire to improve, replace or even do science, the scientific community has determined that their criticisms are invalid a long time ago.

jobby said:

Are people allowed to believe that God or aliens in some way influenced the development of life on earth?

One is free to believe whatever their heart desires, provided it does not lead them to commit crimes. However, if you want your belief taught as a science, you must provide evidence that it is a science, and demonstrate that it has applications in science.

Creationists and Intelligent Design proponents have done neither.

jobby said:

Would asking if there could be a limit to how far natural selection could take the changing of body plans from simple to complex be a valid criticism?

That’s what evolutionary biologists are already trying to do, and if you actually bothered to read their scientific reports, you would have already known this. Furthermore, the suggestions that you have already made are both ridiculous and stupid.

I think you need to go fuck yourself Handjobby. Telling children there are legitimate alternate theories to evolution is the lie, moron. I’m fine, thanks for asking, but you are a lying sack of shit for implying that someone can’t be disgusted with you and be OK. Half-assed snarks are all you are capable of, shit-fer-brains.

What a lying sack of shit you are Handjobby. No one has ever said or implied that anyone should not be allowed to believe any fool thing they want. Do you actually think these moronic questions prove anything? Mentally masterbating in public is in very poor taste. What would the children think?

Oh, and asking a question is not a criticism, moron. No wonder you have so little understanding of what we are talking about, you don’t understand the vocabulary. You shouldn’t have spent so much time making porn doodles in the margins of your English homework. Idiot.

“Would asking if there could be a limit to how far natural selection could take the changing of body plans from simple to complex be a valid criticism?” Why a criticism? This strikes me as the sort of question that can be investigated fruitfully. “…you do admit there is a limit to what NS can do? Or at least the limit or lack of has not been proven yet.” This my understanding: there are two very different sorts of limits to what RM+NS can do. The first has to do with the requirements for life - metabolism, reproduction, etc. It’s nearly tautological that life must be viable. If it’s not, it dies. The second has to do with contingency. There must exist a possible path from some point A to any point B, for that point B to be reached. And so, just through the sorts of variations that just happened to be available to select from throughout biological history, lineages adopted specific evolutionary lines and structures. Just like there are possible bridge hands that have never been dealt, there are body plans that aren’t physically ruled out, but simply didn’t occur. None of the body plans evolution has blundered across so far have been impossible, of course. Some didn’t make it for as long as others.

Apparently double spacing between paragraphs doesn’t work, html tags don’t work, quotations don’t work…I hope my response is comprehensible. I admit defeat on trying to produce anything like a readable format.

Would asking if there could be a limit to how far natural selection could take the changing of body plans from simple to complex be a valid criticism?

Why a criticism? This strikes me as the sort of question that can be investigated fruitfully.

…you do admit there is a limit to what NS can do? Or at least the limit or lack of has not been proven yet.

This my understanding: there are two very different sorts of limits to what RM+NS can do. The first has to do with the requirements for life - metabolism, reproduction, etc. It’s nearly tautological that life must be viable. If it’s not, it dies.

The second has to do with contingency. There must exist a possible path from some point A to any point B, for that point B to be reached. And so, just through the sorts of variations that just happened to be available to select from throughout biological history, lineages adopted specific evolutionary lines and structures. Just like there are possible bridge hands that have never been dealt, there are body plans that aren’t physically ruled out, but simply didn’t occur. None of the body plans evolution has blundered across so far have been impossible, of course. Some didn’t make it for as long as others.

jobby said:

None of the body plans evolution has blundered across so far have been impossible, of course. Some didn’t make it for as long as others.

.… but the point still is: can NS selection account for all the complex body plans in the time frame?

You are not saying there is no speed limit here are you?

could a whale evolve from a land animal in 1000 years??

Why can’t the Administrators ban this one-note, one-hit blunder once and for all? Are they that powerless?

Are people allowed to believe that God or aliens in some way influenced the development of life on earth?

Of course they are, jobby. As a matter of fact, you are even allowed to believe that you are a god, or an alien, or even an alien god. However, if a science teacher wanted to proclaim in science class that he is god and influenced life on earth, would there be a problem? Should there be one?

.… but the point still is: can NS selection account for all the complex body plans in the time frame?

This question is much less straightforward than it sounds.

One way to answer is, very clearly all the body plans currently extant HAVE evolved in the time available, so clearly it’s sufficient time. One might as well ask if the force of gravity is sufficient to pull a dropped brick all the way to the ground. There’s no reason to ask such a question EXCEPT unless one is convinced for utterly unrelated reasons that it can’t be the case, and some increment of magic must be involved.

But if that were true, what means could we conceivably use to test every known process for elements of magic? It could be lurking everywhere!

Another general observation is, when multicelled critters first occurred, there weren’t any existing rules or contingencies. It was free-for-all, anything goes. So there were lots and lots of different approaches, but only slightly different from one another. In principle, each of these tiny variations represented a “different body plan” right from the start, even though evolution hadn’t had nearly enough time to gradually radiate these differences.

Think of a fork in the road. Within only a few feet of that fork, there’s not much distance. You can toss a stone from one fork to the other. BUT these tiny differences eventually result in the roads being very far apart, hard to believe such large differences “had time” to happen. So we look back at the Cambrian with present-colored glasses, imposing on damn-near-identical fossils entirely distinct phyla because they kinda resemble what we knew they’d become in half a billion years.

jobby said:

.… but the point still is: can NS selection account for all the complex body plans in the time frame?

So far the evidence suggests indeed that it could. You were told, you refused to address, you resorted to using multiple aliases and were banned. It’s time to contact your ISP and the library from which you so often post and advise them of the abuse of service.

Sure, many people hold such beliefs, even on this blog. The problem is when religious people let their faith cause them to reject good science for no good reason. Worse, when they refuse to familiarize themselves with evolutionary theory and even worse when they violate the rules of this blog by using sock puppets and then claim “censorship”.

jobby said:

Are people allowed to believe that God or aliens in some way influenced the development of life on earth?

We’ve already answered your inane questions several times before; you just pretend that you haven’t been answered, and that is why we consider you to be an inane and irritating moron.

jobbyMoron lied:

You are powerless to answer these questions. Banning will not change that fact.

Please restrict any further comments to the subject of the essay.

Thanks.

About this Entry

This page contains a single entry by Arthur Hunt published on August 29, 2008 7:07 PM.

Genome Biology: “It is alive” by Gregory A Petsko was the previous entry in this blog.

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