Followup to "dragons and microbes" post

Posted 25 November 2005 by Tara Smith

I discussed here new research on venom evolution that topples some old conventional wisdom. It seems this and another study are already making waves in that field. Genealogy of Scaly Reptiles Rewritten by New Research

The most comprehensive analysis ever performed of the genetic relationships among all the major groups of snakes, lizards, and other scaly reptiles has resulted in a radical reorganization of the family tree of these animals, requiring new names for many of the tree's new branches. The research, reported in the current issue of the journal C. R. Biologies, was performed by two biologists working at Penn State University: S. Blair Hedges, professor of biology, and Nicolas Vidal, a postdoctoral fellow in Hedges' research group at the time of the research who now is a curator at the National Museum in Paris. Vidal and Hedges collected and analyzed the largest genetic data set ever assembled for the scaly reptiles known as squamates. The resulting family tree has revealed a number of surprising relationships. For example, "The overwhelming molecular-genetic evidence shows that the primitive-looking iguanian lizards are close relatives of two of the most advanced lineages, the snakes on the one hand and the monitor lizards and their relatives on the other," Vidal says.

"We gave this group the new name, 'Toxicofera' because of another discovery, reported in a related paper, that some lizard species thought to be harmless actually produce toxic venom, as do some snakes--including some large monitor lizards in the same family as the giant Komodo Dragon and some large species of iguanians." Vidal, Hedges, and other researchers report this and other discoveries about the early evolution of the venom system in lizards and snakes in a paper led by Bryan G. Fry, of the University of Melbourne in Australia, published in the current issue of the journal Nature. "It's a really startling thing that so many supposedly harmless lizards actually are venomous," Vidal comments, "but their sharing of this characteristic makes sense now that our genetic studies have shown how closely they are related."

(More info at the link).

This is a great example of how science works. Important new findings have come to light, and the rest of the evidence is re-examined in that light, to see what stays and what thinking may need to be revised. No one expects it to happen overnight, and a call is put out for others to investigate and test the new conclusions:

"Because the current tree has been widely accepted for nearly a century, I think there is going to be a delay of maybe a few years before the general scientific community gets used to the new tree," Vidal says. "If other research groups working in this area find the same pattern with additional genes, then I believe the scientific community may accept these results more quickly."

Note how there are no politics involved, no pressure to teach these new results. The investigators are confident enough in their own data that they can wait for other scientists to examine it, express skepticism, test it themselves, and add their own conclusions to the scientific literature. It may take several years, but if the data stand up and are repeated by others, the way students are taught *will* change--not because anyone was lobbied to do so, but because the evidence is strong and it would be folly not to acknowledge that. I look forward to following this in the coming years.

68 Comments

Ed Darrell · 25 November 2005

Do these guys plan to go before the Ohio State Board of Education to argue their results?

It's crazy, I know: But perhaps someone in Ohio should urge that the Board hold a hearing on these results. The same in Kansas. Wouldn't it be delicious to see the creationists squirm?

Pete Dunkelberg · 25 November 2005

The phylogeny of squamate reptiles pdf online

images

BlastfromthePast · 25 November 2005

It may take several years, but if the data stand up and are repeated by others, the way students are taught *will* change---not because anyone was lobbied to do so, but because the evidence is strong and it would be folly not to acknowledge that. I look forward to following this in the coming years.
— Tara Smith

Tara, while I applaud your optimism, I note two things: (1) you mention the need to "repeat" this work. That's going to take time. And....it might be then that "controversy" sets in. Which means that this might not be "taught" for some time. But, let's assume all goes well. Then (2) you'll note that the "primitive-looking iguanian lizards are close relatives of two of the most advanced lineages, the snakes on the one hand and the monitor lizards and their relatives on the other." This would seem to imply that "scientists", for at least the last century, have made all kinds of judgments based on what things "looked like." How much more is there, then, that is assumed to be the "way things are" and yet is based on simplistic, subjective judgments? While you might laud this "scientific" approach to knowledge, it points out that a lot of paleontology just might turn out to be built on a house of cards. And, to RDLenny Flank, again, did you notice they've now found "venom" genes in lizards?! And what about amphibians--they're likely candidates for venom. If found in amphibians as well, then that pushes us back to the fishes. Could it be that there are some fish out there that also produce venom? Where will it all end?

kswiston · 25 November 2005

Where does this leave the Agamids, like my little Mali Uromastyx? I know they used to be considered a sister taxa to Iguanas based off morphology similarities, but is that still the case?

kswiston · 25 November 2005

Scientists had no choice but to classify organisms based on morphology 100 years ago, because molecular/genetic comparison studies weren't possible until somewhat recently. You can't expect classical scientists to have considered genetic relationships when assigning animals to various taxa when genetics didn't even exist at the time.

Also, you must not be familiar with comparative morphology studies because they're not equivalent to saying "Well A looks like B, so they must be related". Good morphology studies take multiple morphological features into consideration. Of course, convergent evolution can lead to some uncanny similarities in morphological features of two independently evolved structures, so basing taxonomic relationships strictly on morphology will lead to mistakes.

And, to RDLenny Flank, again, did you notice they've now found "venom" genes in lizards?! And what about amphibians---they're likely candidates for venom. If found in amphibians as well, then that pushes us back to the fishes. Could it be that there are some fish out there that also produce venom? Where will it all end?"

Not all lizards have venom genes, and since venom is not a trait of the common ancestor of Squamata, it's evolution can't be pushed back into amphibians or fish.

kswiston · 25 November 2005

How do you get the quote tag to work??? I can't seem to figure it out for some reason.

Anyhow,

Blast Said: "Tara, while I applaud your optimism, I note two things: (1) you mention the need to "repeat" this work. That's going to take time. And....it might be then that "controversy" sets in. Which means that this might not be "taught" for some time. But, let's assume all goes well. Then (2) you'll note that the "primitive-looking iguanian lizards are close relatives of two of the most advanced lineages, the snakes on the one hand and the monitor lizards and their relatives on the other." This would seem to imply that "scientists", for at least the last century, have made all kinds of judgments based on what things "looked like." How much more is there, then, that is assumed to be the "way things are" and yet is based on simplistic, subjective judgments? While you might laud this "scientific" approach to knowledge, it points out that a lot of paleontology just might turn out to be built on a house of cards."

Blast also said:"And, to RDLenny Flank, again, did you notice they've now found "venom" genes in lizards?! And what about amphibians---they're likely candidates for venom. If found in amphibians as well, then that pushes us back to the fishes. Could it be that there are some fish out there that also produce venom? Where will it all end?"

Not all lizards have venom genes, and since venom is not a trait of the common ancestor of Squamata, it's evolution can't be pushed back into amphibians or fish.

k.e. · 25 November 2005

Hey Blast
Did you ever find out what ailed Parsifal ?

limpidense · 25 November 2005

"...built on a house or cards" laments BftP with the falsest of crocodile tears! "Where will it all end?"

[edited by Tara]

We can do without the insults, please.--T

Dr. Bryan Grieg Fry · 25 November 2005

> BlastfromthePast wrote: did you notice they've now found "venom" genes in lizards?! And what about amphibians---they're likely candidates for venom. If found in amphibians as well, then that pushes us back to the fishes. Could it be that there are some fish out there that also produce venom? Where will it all end?

I don't think you understand where venom comes from. Have a read of our paper in Genome Research earlier this year
http://www.venomdoc.com/downloads/2005_BGF_Genome_2_Venome.pdf
Venom toxins are not created out of thin air. Rather they are the result of a duplication of a body protein, often one involved in a crucial physiological process such as blood coagulation, this duplicate is then selectively expressed in the venom gland followed by subsequent venom gland specific diversification of the gene. The toxic mutants are used to catastrophically disrupt the physiology of the prey item.

We already have venomous fish, such as catfish, stonefish, stingrays, Port Jackson sharks etc. The venom in fish is an independent evolution, the dorsal and pectoral spines being non-homologous structures relative to the oral venom of reptiles. Similarly, spiders are independent origin, as are scorpions, blue-ring octopus, primate such as slow lorises, other mammals such as shrews and platypus, etc. Venom has been independently evolved in most of the major lineages.

So I utterly fail to see your point. Can you clarify?

Au revoir
Bryan

dre · 25 November 2005

Dr. Fry,

Word up. We are all bettered when clarifications are made in a clarifying way.

Keep on truckin'.

Norman Doering · 25 November 2005

kswiston wrote:

it's evolution can't be pushed back into amphibians or fish.

But there are toxic and venomous fish: Puffer fish (fugu in Japan, zombie toxin in "Serpent and the rainbow"), Anemones, the Lionfish... Some Rays have a sharp spine at the end of the tail and poison gland are spaced along the teeth of the spine. Where do they fit in? The tetrodotoxin found in puffer fish is also in some toads and in the saliva of the blue-ringed octopus. It inhibits sodium transport, affects neuronal transmission in the central and peripheral nervous system and also cardiac nerve conduction and contraction. I don't think the toad, puffer fish and octopus are evolutionary cousins.

Red Mann · 25 November 2005

Hey Blast! Keep up the good work. S&A Red

'Rev Dr' Lenny Flank · 25 November 2005

And, to RDLenny Flank, again, did you notice they've now found "venom" genes in lizards?!

And to Blast again, did you notice that none of them are modern snake venoms? I also noticed that you neglected to bring up the topic with Dr Fry when given the chance ----- wassamatter, Blast, afraid that someone who actually studies the topic will show the whole world how pig-ignorant you really are? C'mon, Blast --- go ahead and tell Dr Fry all about your "frontloading" BS. He could use the laugh, and the rest of us would thoroughly enjoy watching your pompous little tookus getting kicked across the room. Coward.

'Rev Dr' Lenny Flank · 25 November 2005

I don't think you understand where venom comes from.

Actually, Blast thinks that YOU (and ll other "evolutionoists) don't understand. See, Blast has been reading some hundred-year-old science (Goldschmidt, mostly) along with his Dembski religious tracts, so Blast has convinced himself that there are really no "new" genes --- they are all just different combinations of the genes that were originally present in each "kind" (or maybe in the first life form -- Blast is a little vague about that). So, Blast has convinced himself that the venom genes in amphibians, fish, lizards and snakes are all just THE VERY SAME GENES, re-arranged a bit in each species. Blast calls this "frontloading". G'head, Blast. Tell Dr Fry all about it. (snicker) (giggle)

Flint · 25 November 2005

I guess I'll answer Blast once again, because he takes what might be valid points, and instead uses them for purposes of innuendo without ever coming out and identifying his objective.

This would seem to imply that "scientists", for at least the last century, have made all kinds of judgments based on what things "looked like."

Not "all kinds of judgments" but rather "best fit" tentative organization based on the best data available at the time. I THINK Blast is trying to imply (without actually saying it) that these weren't really scientists (otherwise why the scare quotes?), that they were plain guessing, and that this new information illustrates that their guesses were worthless. By extension, *anything* based on the best observations available at the time are worthless guesses, showing that evidence is a worthless foundation on which to base conviction.

How much more is there, then, that is assumed to be the "way things are" and yet is based on simplistic, subjective judgments?

We tentatively (a concept mystical to Blast) classify things according to what we have learned. There's always more to learn, and classifications are always subject to change. This is the only way ever devised to get things more nearly correct. But if the evidence points (tentatively but strongly) in one direction, why is it "simplistic" and "subjective" to conclude that the evidence MEANS something, subject to more and better evidence perhaps leading to different, better-informed *but still tentative* conclusions? Blast is assuming the need (his own need) for absolutes. Oops, better evidence indicates that some tentative conclusions weren't entirely correct. For Blast, this means they were absolutely wrong. For Blast, "totally wrong" is the ONLY alternative to the kind of perfect knowledge that evidence cannot provide, but faith can.

While you might laud this "scientific" approach to knowledge, it points out that a lot of paleontology just might turn out to be built on a house of cards.

And there we are. If it's not absolutely correct, beyond any even theoretical possibility of improvement, then it's a "house of cards." I can only suggest to Blast that a scientific paleontologist is ALWAYS looking for something better. Science, as a discipline, *assumes* that every bit of our knowledge is imperfect. Otherwise, why bother looking at all? Why not just grab any handy scripture, declare ourselves an interpretation and worship it? That's the key to absolutes, after all -- we would be both absolutely certain, and absolutely wrong. Absolutely forever.

Pete Dunkelberg · 25 November 2005

limpidense,
your reply to Blast is offensive. If you can't contribute pure reason, that's OK. Lots of people can't. Please don't try to compensate by making personal attacks.

Ed Darrell · 25 November 2005

A poster calling himself Blastfromthepast said:

This would seem to imply that "scientists", for at least the last century, have made all kinds of judgments based on what things "looked like." How much more is there, then, that is assumed to be the "way things are" and yet is based on simplistic, subjective judgments? While you might laud this "scientific" approach to knowledge, it points out that a lot of paleontology just might turn out to be built on a house of cards.

Simplistic and subjective? No, not at all. Judgments based on the best information available. And tell us, Mr. Blastfromthepast: What has been the harm of making those judgments in the past? The only issue here is exactly how closely some reptilians are related to other reptilians. The new information just makes our research more accurate -- it doesn't mean anything in the past was inaccurate. At worst, the previously-thought lines of relationship may have prevented us from seeing relationships that might make for future family-based antivenins. With new knowledge, we may be able to speed development of antidotes for venom, or find new applications for natural substances to make new pharmaceuticals. Where, do you claim, was there any harm in getting the answers close before, but not exactly right? Are arguing that we should never claim anything as known unless everything is known? Can we not claim your sibling as the product of your shared parents unless we test all 6 billion other people on Earth to make sure no one is more closely related?

Dr. Bryan Grieg Fry · 25 November 2005

Blastfromthepast, you seem to be confusing a few things. Past arrangements were undertaken using the best tools of the time. The Human Genome Project has been the classic leading edge customer, making technology (that fifteen years ago was science fiction) affordable to ordinary researchers. Thus, we are currently in a major taxonomical 'cleanup' era. The DNA studies allow for additional insights into the evolution of the animals.

Of course, if someone doesn't believe in evolution this will all be lost to them.

Cheers
Bryan

Michael Hopkins · 25 November 2005

kswiston, to make a quote:

<quote> Text to quote </quote>

<quote author="some guy"> Text to quote </quote>

And don't put in any tag called "KwickXML".

Jaime Headden · 26 November 2005

Unfortunately, this does decide to ignore or overwrite nomenclature established for other authors that anyone familiar with "supraordinal" taxonomy of mammals may be familiar with. Terms like Scleroglossa, Scincomorpha, Lacertoidea, Teiioidea, and Scincoidea are largely ignored. Vidal and Hedges similarly replaced some potential definitions of names with new terms, instead of just using the existing term for the position they gave. Scinciformata is the same as Scincoidea, Teiiformata is the same as Teiioidea when the content of the groups are evaluated. Their reasoning almost solely based on the implication that "oidea" and "formata" suggest different things to the readers. The analysis is also the same as that published in Fry et al., of which Vidal was a coauthor, so it is likely the gene expert S. Blair Hedges was recruited to publish on the phylogeny and nomenclature, as well as the broader implications of the analysis, based on nuclear genes including one of the Hox genes.

I am curious if anyone knows of HOX genes used in other analyses.

EZGoing · 26 November 2005

Finally a controversy I know something about!
kswiston, I think Michael Hopkins is all wrong. Use "blockquote" instead. :)
(I didn't even know about "quote"; That'll save me a lot of typing.)

k.e. · 26 November 2005

A BLAST calling himself POSTfromthepast said:

This would seem to imply that "~~scientists~~Fundamentalist's(literal readers of Genesis)", for at least the last century, have made all kinds of ~~judgments~~ statements of fact based on what things "~~looked like.~~are" How much more is there, then, that is ~~assumed~~ known to be the "way things ~~are~~ were" and yet is based on simplistic, ~~subjective~~objectivist* judgments? While you might laud this "~~scientific~~LITERAL READING OF GENESIS" approach to ~~knowledge~~ truth, it points out that a lot of ~~paleontology~~ GENESIS and "The Word^TM, just might turn out to be built on a house of cards.

Thank you POSTfromthe past for those readings from the cognitive dissonance of "The Word",^TM we will stick to the TRUTH. objectivist 1.Philosophy. One of several doctrines holding that all reality is objective and external to the mind and that knowledge is reliably based on observed objects and events. 2.An emphasis on objects rather than feelings or thoughts in literature or art. objectivism = "the idea that all acceptable knowledge must take the form of exact, impersonal, context-neutral 'facts'" p.1 related to Modernity results in 'hyper rationalistic technocratic tyranny' - "History is Bunk" >>>>"BRAVE NEW WORD" Huxley's revenge relativism = the opposite, or ultimate conclusion, where "no knowledge claims of the objectivist kind can be found, there is no true knowledge and rival knowledge claims are incommensurable". p.1 related to late-Modernity or sometimes Post-Modernity. results in 'deconstructive irrationalistic nihilism'. Equal time for the "controversy" >>> "1984" Orwell's revenge "false gods= false truth".

Neal · 26 November 2005

Any theory that purports to be scientific must somehow, at some point, be compared with observations or experiments. According to a 1998 booklet on science teaching issued by the National Academy of Sciences, "it is the nature of science to test and retest explanations against the natural world." Theories that survive repeated testing may be tentatively regarded as true statements about the world. But if there is persistent conflict between theory and evidence, the former must yield to the latter.
Jonathan Wells

David Harmon · 26 November 2005

LimpidDense: Nice riffs! (lessee, Twain, ???, Parker? or has my tin ear gone rusty?)

Speaking of the taxonomy of toxic species: Where would Blastt fit into the tree? How about that JBHandley twit who just "punk'd" Orac et al? :-)

Stephen Elliott · 26 November 2005

Posted by David Harmon on November 26, 2005 09:13 AM (e) (s)... Speaking of the taxonomy of toxic species: Where would Blast fit into the tree?...

Blast's venom is more of an irritant than a poison. So not sure if he could be classified as toxic.

'Rev Dr' Lenny Flank · 26 November 2005

Any theory that purports to be scientific must somehow, at some point, be compared with observations or experiments.

Excpet ID, apparently. After all, IDers do no experiments or observations of any sort to test any of their, uh, scientific hypotheses. Mostly, all they do is quote-mine the work of scientists who ARE doing experiments and observations. Just like the creation "scientists" did.

'Rev Dr' Lenny Flank · 26 November 2005

At the end of the Washington Monument rally in September, 1976, I was admitted to the second entering class at Unification Theological Seminary. During the next two years, I took a long prayer walk every evening. I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father's many talks to us, and through my studies. Father encouraged us to set our sights high and accomplish great things. He also spoke out against the evils in the world; among them, he frequently criticized Darwin's theory that living things originated without God's purposeful, creative activity. My studies included modern theologians who took Darwinism for granted and thus saw no room for God's involvement in nature or history; in the process, they re- interpreted the fall, the incarnation, and even God as products of human imagination. Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle. As a graduate student at Yale, I studied the whole of Christian theology but focused my attention on the Darwinian controversies. I wanted to get to the root of the conflict between Darwinian evolution and Christian doctrine. In the course of my research I learned (to my surprise) that biblical chronology played almost no role in the 19th- century controversies, since most theologians had already accepted geological evidence for the age of the earth and re-interpreted the days in Genesis as long periods of time. Instead, the central issue was design. God created the cosmos with a plan in mind. This affirmation is among the most basic in all of Christianity (and other theistic religions as well, including Unificationism). And that plan included human beings as the final outcome of the creative process: we are created in the image of God. --Jonathan Wells, "Darwinism; Why I Went for a Second PhD"http://www.tparents.org/Library/Unification/Talks/Wells/DARWIN.htm Note: By "Father", Wells is referring to Rev Sun Myung Moon. Yeah, the wacko cult guy. Wells has been a member for over 30 years.

Does that sound even remotely "scientific" to you? Me neither. Does it sound like a cult religious crusade against evolutionary biology to you? Yep, me too.

BlastfromthePast · 26 November 2005

So I utterly fail to see your point. Can you clarify? Au revoir Bryan
— Dr. Bryan Grieg Fry

You'll have to indulge us, Dr. Fry, but Lenny and I were having, let us say, a little discussion about the results of your work. I have a very jaundiced opinion of Darwinian evolution, though not to common descent; and I'm sympathetic to ID. One of the things that ID could suggest--and it's simply hypothetical--is the "front-loading" of genes: that is, that the expressed genes of both pro-and eu-karyotes were there already from the beginning: a "tool box", if you will. At first glance that might seem preposterous, if not for the fact that the coding portion of DNA is such a small percentage of the total DNA. Let me just add, the idea of this "front-loading" is plausible, maybe even possible, but certainly not anything that ID requires, nor anything for which weighty evidence has been found. In RDLenny Flank's attempts to ridicule ID, he has taken the position that if "front-loading" is true, then where is the "gene for snake venom" in other lineages. Actually, if I'm not mistaken, it was the article that you cite that was the cause of our "discussion." I indicated that (from memory now) your article gave evidence that one type of snake venom is actually a gene for saliva that has been transformed in some way. I used that as a rebuttal, arguing that if venom could be produced by a transformation of existing saliva genes, then maybe looking for snake venom in other genomes is a useless task. In other words, if you looked for "venom", you wouldn't find it, for it would simply be "hiding" as a "saliva gene" and no more; and that what would then be critical, would be the possible presence of a regulatory gene controlling that part of the snake genome that codes for the "transformation" of the saliva. (Is the idea of some "transformation" gene, along with its complimentary regulatory gene, present in the various lineages that produce venom, but lying, for the most part, unexpressed, a possibility at all?) Sorry to drag you into this. I was really just having a little fun with Lenny.

And tell us, Mr. Blastfromthepast: What has been the harm of making those judgments in the past? The only issue here is exactly how closely some reptilians are related to other reptilians. The new information just makes our research more accurate --- it doesn't mean anything in the past was inaccurate.

I'm not throwing rocks at evolutionary theory here. It's understandable that revision is necessary; and that those who made the conclusions they did, did so with best knowledge and judgment available to them. My words are words of caution. Tara is applauding how evolutionary science works. Fine enough. But there's this flip side. And that flip side is that a fair amount of "cleaning up" of what is "known" needs to take place. What I'm saying here verges on criticism, but is perhaps not; it is more in the form of an observation which leads to a word of caution. I'm going to refrain from any further comments on the board lest it gets way off topic. I don't think that's fair to Tara.

BlastfromthePast · 26 November 2005

The DNA studies allow for additional insights into the evolution of the animals.
— Dr. Bryan Greig Fry

I'm very curious about the search methods you use. Is your method, to take snake venom, e.g., break down the protein into its string of A.A.'s, to then translate that into code, and then finally to search various genomes looking for anything similar (anything "similar" meaning that you use some statistical test for, let us say, "closeness of match")? Is that a fair enough assessment of the methods currently being used?

BlastfromthePast · 26 November 2005

Sorry for the three posts in a row, but I forgot to ask this question.

It's for anyone, but Dr. Fry, you might have an immediate answer for this: what is the best book on Evo-Devo out there right now?

'Rev Dr' Lenny Flank · 26 November 2005

In RDLenny Flank's attempts to ridicule ID, he has taken the position that if "front-loading" is true, then where is the "gene for snake venom" in other lineages.

No, Blast, that's NOT what I said. Don't be a liar. What I said was "where is the gene for cobra venom in a garter snake"? After all, Blast, it was YOUR silly assertion that all possible snake venom genes were present in the very first snake, and just "recombined" afterwards. So, SHOW us.

'Rev Dr' Lenny Flank · 26 November 2005

I'm not throwing rocks at evolutionary theory here. It's understandable that revision is necessary; and that those who made the conclusions they did, did so with best knowledge and judgment available to them. My words are words of caution. Tara is applauding how evolutionary science works. Fine enough. But there's this flip side. And that flip side is that a fair amount of "cleaning up" of what is "known" needs to take place. What I'm saying here verges on criticism, but is perhaps not; it is more in the form of an observation which leads to a word of caution.

Hey Blast, would you mind pointing to any of this "cleaning up" that has been done by ID? (sound of crickets chirping) Hey Blast, would you mind pointing to ANY scientific discovery, of any note, in any area of science, made at any time in the past 25 years as the result of ID "research"? (sound of crickets chirping) Gee, I wonder why that is . . . . . .

I'm going to refrain from any further comments on the board lest it gets way off topic. I don't think that's fair to Tara.

Oh, puh-leeze . . . .

'Rev Dr' Lenny Flank · 26 November 2005

I indicated that (from memory now) your article gave evidence that one type of snake venom is actually a gene for saliva that has been transformed in some way.

Um, that "some way" is called "evolution", Blast. Perhaps you've heard of it?

Neal · 26 November 2005

First off, what about Behe's experiments?

Second, what are the evolutionist experiments? Other than the ones that were rigged, or the fossils that were outright faked?

'Rev Dr' Lenny Flank · 26 November 2005

First off, what about Behe's experiments?

Um, what experiments would those be . . . .

Second, what are the evolutionist experiments? Other than the ones that were rigged, or the fossils that were outright faked?

Um, such as . . . . ?

Dr. Bryan Grieg Fry · 26 November 2005

> I'm very curious about the search methods you use. Is your method, to take snake venom, e.g., break down the protein into its string of A.A.'s, to then translate that into code, and then finally to search various genomes looking for anything similar (anything "similar" meaning that you use some statistical test for, let us say, "closeness of match")?

No.

We sequenced nuclear genes of the various lineages which allowed us to construct a phylogenetic tree of the relationships of the animals themselves.

Parallel to this we constructed cDNA libraries of the venom glands themselves and sequenced clones. This provided information as to what was being transcribed in the venom glands. Phylogenetic analyses of the transcripts, previously characterised venom toxins and related body proteins allowed us to determine which toxin types were the result of a single origin. Mapping these results over the phylogenetic tree of the animals themselves provided insights as to the relative timing of recruitment events for the various toxin types.

We did not search genomes for homologs but rather showed that they were actually being made in the venom glands.

If I understand it correctly, the frontloading hypothesis does not allow for the origin of new protein types through the mutation of previous molecular scaffolds. However, we see extensive evidence of that just in the venom components where the ancestral body protein gene has been mutated in such dramatic ways that entirely new protein types have been developed. The amount of new genomic information can be quite considerable as a result of this accelerated protein evolution though rapid gene duplication and diversification of the venom gland specific genes. Within the body, similar sorts of protein evolution has occurred. The frontend hypothesis is fatally flawed since it does not allow for the accumulation of new information.

As for venoms being the same in different lineages, this is completely wrong. Fish venom proteins are radically different than snake venom proteins, just are spider venom proteins etc. They have nothing in common other than hurting like hell!

Cheers
Bryan

Moses · 27 November 2005

Comment #60229 Posted by Neal on November 26, 2005 06:40 PM (e) (s) First off, what about Behe's experiments?

Widely discredited intellectual masturbation doesn't count as an "experiment."

Second, what are the evolutionist experiments? Other than the ones that were rigged, or the fossils that were outright faked?

Yes, the well-funded, vast left-wing-"Evilutionist" conspiracy and 150 years of fakery that only a select enlighted (but remarkably uneducated in the field) individuals can detect. If there was a "stupid post of the month award" this would be front runner. Not because of its complexity, but its minimalist approach illustrating the opposition.

k.e. · 27 November 2005

Yeah the attack of the (miniature)Killer Green Tomatoes

Don S · 27 November 2005

"If there was a "stupid post of the month award" this would be front runner."
— Moses

The great thing about PT - and IDers just don't get this - you ask a stupid question, you get a smart answer. Tara, thanks for the great articles, and thanks Dr. Fry, for your measured responses. Every day, a rank amateur like me can come learn something new and exciting, and be entertained by the clowns in the other rings at the same time. What more could you ask for?

byzanteen · 27 November 2005

"of dragons and microbes" - isn't that a bit redundant? After all, aren't microbes just teeny tiny dragons?

RPM · 27 November 2005

BlastFromthePast:

Start with Ohno's Evolution by Gene Duplication, then read some of the reviews by Lynch and Long. Maybe then you will understand that there is no "frontloading" -- the only frontloaded information is the ancestral copy of a gene that was duplicated and one copy evolved a new function.

Troll · 27 November 2005

Wow! Similarity as evidence for evolution! Man, the evidence is overwhelming! How can anyone deny evolution in the face of such overwhelming evidence?!?!

k.e. · 27 November 2005

Similarity as evidence for telling the Similarity and dis-Similarity between any 2 items of same.

The quality or condition of being similar; resemblance. See Synonyms at likeness.
A corresponding aspect or feature; equivalence: a similarity of writing styles.

Synonyms:
likeness,agreement ,comparison,conformity,consistency,copy,correspondence
duplicate,equivalence

antonyms:
falseness, impossibility,disagreement, dissension,, incongruity,inconsistency,divergence, imbalance

Synonym:
1.A word having the same or nearly the same meaning as another word or other words in a language.
2.A word or an expression that serves as a figurative or symbolic substitute for another.
3.Biology. A scientific name of an organism or of a taxonomic group that has been superseded by another name at the same rank.

antonym:
A word having a meaning opposite to that of another word

Did you fail English as well as Science ?
How are you able to determine what TRUTH is ?
IF You are unable to find the TRUTH how do tell what is FALSE ?
what does the Bible say about false Gods ?
Does the Bible tell you God is True ?
Some people are lying to you they are not gods they are false gods.
I feel sorry for you.

Arden Chatfield · 27 November 2005

k.e. (and others):

I really do not think we should be feeding Troll.

'Rev Dr' Lenny Flank · 28 November 2005

Alas, Blast seems to have tucked tail and made a hasty departure . . . .

AC · 29 November 2005

Oops, better evidence indicates that some tentative conclusions weren't entirely correct. For Blast, this means they were absolutely wrong. For Blast, "totally wrong" is the ONLY alternative to the kind of perfect knowledge that evidence cannot provide, but faith can.
— Flint

Revenge of the Platonists, guys. There is room enough in the human mind for all things to roam. The real, physical, mutually observable world, however, is...much less forgiving. Those willing to embrace and explore this disparity, rather than fearfully reject it, harness the greatest power of humanity. Meanwhile, this research (including Dr. Fry's supplimentary comments in this thread) is fascinating.

BlastfromthePast · 30 November 2005

We did not search genomes for homologs but rather showed that they were actually being made in the venom glands. If I understand it correctly, the frontloading hypothesis does not allow for the origin of new protein types through the mutation of previous molecular scaffolds. However, we see extensive evidence of that just in the venom components where the ancestral body protein gene has been mutated in such dramatic ways that entirely new protein types have been developed. The amount of new genomic information can be quite considerable as a result of this accelerated protein evolution though rapid gene duplication and diversification of the venom gland specific genes. Within the body, similar sorts of protein evolution has occurred. The frontend hypothesis is fatally flawed since it does not allow for the accumulation of new information.

Thank you, Dr. Fry, for your response. I see that you did not search the genomes for "homologs". That clears the way for a follow-up regarding "frontloading." Front-loading is simply a working hypothesis. As a hypothesis, it doesn't require that the gene for a particular protein be present--in its entirety--from the beginning. Nor does it require that genes remain static over time, it simply means that the kind of "information", that you refer to, is present from the beginning. So, for example, in this instance, is it (hypothetically) possible that we have a suppressed Hox gene (present in the genomes of all eukaryotes) that becomes "un-suppressed" in venomous animals, with this Hox gene adding on--perhaps at the end of one kind of body protein or another--an amino acid sequence that proves highly toxic (as, e.g., happens with to saliva in some lizards)? [As to the Hox gene being present without it being known, let's remember that most of what we know is contained in a genome comes from what is "coded" from that genome. And, if the Hox gene is "suppressed", it is, of course, not coded; and, so, might simply remain undetected.] Could an experiment be run looking for such a "Hox gene" in those lineages which are venomous? [The presence of a Hox gene might help explain why these various proteins have nothing in common other than hurting like hell!!]

Steviepinhead · 30 November 2005

I admit it: there have been plenty of times when I have taken a perverse pleasure in Blast's embarrassing posts--they demonstrate so well the limitless ability--nay, the undeniable urge!--to distort any evidence (no matter how strong or pervasive) in order to avoid the plain inferences in support of evolution.

But I'm now getting to the point where I simply cringe with embarrassment in Blast's behalf.

Empathetic embarrassment--pitiful I know: if it doesn't bother him, why should I let it bother me? But that's still how a post like this makes me feel.

It'll be hours yet before Lenny comes aboard and can slap me back to sanity. Anybody else willing to volunteer?

Aureola Nominee, FCD · 30 November 2005

Steviepinhead:

* slap *

Don't thank me, pal; you'd do the same.

;-)

Steviepinhead · 30 November 2005

Steviepinhead (ruefully rubbing side of head):

"Thanks, Aureola..."

qetzal · 30 November 2005

So, for example, in this instance, is it (hypothetically) possible that we have a suppressed Hox gene (present in the genomes of all eukaryotes) that becomes "un-suppressed" in venomous animals, with this Hox gene adding on---perhaps at the end of one kind of body protein or another---an amino acid sequence that proves highly toxic (as, e.g., happens with to saliva in some lizards)?
— BlastFromThePast

Not really. Hox genes don't add amino acids to other proteins, they determine whether certain genes get turned on or off, e.g. in certain tissues. In any case, this doesn't make sense, because venom proteins don't get made by adding additional amino acids to some other body protein. Venom proteins are fully coded by venom genes, just as other proteins are encoded by their genes. Instead, you could argue that some unknown gene codes for a protein that "creates" venom genes by adding extra codons to the DNA of some other, pre-existing gene. That would at least fit with how toxin genes are transcribed and translated into proteins. But the extra codons have to come from somewhere. If they're present elsewhere in the genome, they'd be detectable. If they're not, where do they come from? Would this hypothetical codon-adding protein generate the specific DNA sequence without reference to any other nucleic acid template? That would be extraordinary, as there's no evidence for such a process anywhere in biology (that I know of). Doesn't mean it's impossible, but absent any supporting evidence, it's extremely unlikely.

[As to the Hox gene being present without it being known, let's remember that most of what we know is contained in a genome comes from what is "coded" from that genome. And, if the Hox gene is "suppressed", it is, of course, not coded; and, so, might simply remain undetected.]

A suppressed gene is still there, and still coded. It just isn't being transcribed into mRNA, so the protein that it encodes isn't being made. If a gene is "there," the information it represents has to be coded somewhere and somehow. The only way we know of for that is the standard triplet code in DNA. That code is readily detectable, regardless of whether the gene is suppressed. Hypothetically, of course, there could be another, totally different way to code a gene - i.e., a code that we don't know to look for. But there's no current evidence to suggest such an undiscovered code. P.S. It's pretty clear you don't yet have a good grasp on basic molecular biology. There's no shame in that, but you might not want to use phrases like "of course" when it comes to topics that you don't yet understand well.

Dr. Bryan Grieg Fry · 30 November 2005

>So, for example, in this instance, is it (hypothetically) possible that we have a suppressed Hox gene (present in the genomes of all eukaryotes) that becomes "un-suppressed" in venomous animals, with this Hox gene adding on---perhaps at the end of one kind of body protein or another---an amino acid sequence that proves highly toxic (as, e.g., happens with to saliva in some lizards)?

As I mentioned before, venom toxins are NOT modified salivary proteins. Rather they are the mutation of a normal body protein for the use as a toxin. There is not a magic little amino acid sequence added on but rather changes to existing functional residues or rearrangement of molecular scaffold. All of which is new information as this is occuring on a duplicate gene to the normal body protein, not to the body protein itself.

Venom evolution is much easier to understand if you follow the data trail rather than trying to shoe-horn it into a prepackaged theory that is particularly useless.

In other words, read the papers I've already referenced above.

Cheers
Bryan

ben · 30 November 2005

I admit it: there have been plenty of times when I have taken a perverse pleasure in Blast's embarrassing posts---they demonstrate so well the limitless ability---nay, the undeniable urge!---to distort any evidence (no matter how strong or pervasive) in order to avoid the plain inferences in support of evolution.

Of course it's not just him; he's just one of a bottomless supply of theist dorks who must lay awake at night, unable to accept that there are people who just aren't interested in buying in to their particular superstition-based theories of life, the universe and everything. So they wake up the next day and head out to foist their anti-intellectual hokum on the evil materialsts and rationalists of the world by any means necessary--often trying to co-opt the tools and terms of science as weapons against it, as in Blast's case. It's interesting that one of the principal arguments these people often use against "materialism" is that science is a kind of religion, and they accuse people of "believing" in evolution (for example) in the same way they believe in their gods. But imagine the outrage, the outcry, the accusations of antireligious bigotry and discrimination, if the evil materialists show up on the christian discussion boards and try to tell them their beliefs are ill-founded, bogus, and pathetically out of step with observable reality. Of course, we don't have to imagine, they do it every day, in response to the scientific community even having the gall to try to defend itself against these attempts to dishonestly use science for religious ends.

'Rev Dr' Lenny Flank · 30 November 2005

(sigh)

Blast, you're blithering again.

'Rev Dr' Lenny Flank · 30 November 2005

In other words, read the papers I've already referenced above.

Dude, Blast has already cut-and-pasted abstracts from papers on venom evolution. It was crushingly obvious that he didn't understand a single word. (shrug) If you're attemtping to open Blast's mind, forget it --- he has a soundproof head. Far better to just point out to all the lurkers here how and why Blast repeatedly inserts his head into his, uh, well, you get it.

'Rev Dr' Lenny Flank · 30 November 2005

But I'm now getting to the point where I simply cringe with embarrassment in Blast's behalf.

Indeed, there are times when *I* am tempted to feel sorry for the fundies. It must be terrible to go through life with such crashing insecurities that one not only cannot PERSONALLY tolerate any challenge to the validity of their most cherished beliefs, but also do not want ANYONE ELSE to hear those challenges either. But, whenever I am tempted to feel sorry for fundies, I ask myself to remember that they are all self-righteous smug arrogant pricks who think, quite literally, that they are holier than everyone else, to the extent that, like the Taliban and the Iranian Ayatollahs, they have the divine right -- nay, the divine DUTY -- to eliminate democracy, place themselves in power over us, and be our godly super-nannies to save us all from Satan's temptations, whether we like it or not. That clears up any sympathy I might have for their little feelings.

Steviepinhead · 30 November 2005

Steviepinhead (ruefully rubbing other side of head):

"Thanks, Lenny! I feel much more, um, clearheaded now."

And, since that takes care of both sides of my head for now (and, no, you don't want to slap a pinhead on top of the head), the rest of you will have to wait your turn to chastise me till another day!

BlastfromthePast · 1 December 2005

In other words, read the papers I've already referenced above.
— Dr. Bryan Grieg Fry

I've looked over the paper. Could you explain what you mean by "recruiting"? As well, you mention papers--i.e., plural. Is there another paper/papers you cited? If so, I don't see them on this particular post.

Dr. Bryan Grieg Fry · 1 December 2005

>I've looked over the paper. Could you explain what you mean by "recruiting"?

Here's one of my papers that goes into toxin recruitment events quite in some detail:
The most recent paper also goes into relative timing events of the basal toxin types:
Another paper goes into how examing toxin phylogeny, insights into the evolution of the animals can be elucidated:
Cheers
Bryan

BlastfromthePast · 1 December 2005

Dr. Fry, thanks for the "reading assignment". ;)

'Rev Dr' Lenny Flank · 1 December 2005

Dr. Fry, thanks for the "reading assignment". ;)

Have an educated person explain all the big words to you, Blast. Assuming you even read it. After all, we have not forgotten that YOU were the one who wanted to run off at the mouth all about how whale evolution was wrong, but never heard of _Pakicetus_, and then compounded that with another round of verbal diarrhea about bird evolution, while not knowing what _Caudipteryx_ is. Do you wonder why you get mocked, Blast? Do you wonder why everyone thinks you're an uninformed blowhard, Blast? Wonder no longer.

Steviepinhead · 1 December 2005

Speaking of birds and Blast, a new Archaeopteryx fossil with exquisitely-preserved feet has been found. In previous finds, the feet were fairly scrunched up. Because there were enough other bird-like features, the less faithfully-preserved feet were assumed to be bird-like as well, with a rear-pointing toe.

It turns out that that toe actually points forward, and is set off to one side, strongly resembling the arrangement of toes of Velociraptor and similar dinosaurs.

Thus, Archaeopteryx turns out to be even more of a mosaic of bird and dino features than previously thought. You might even call it a transitional fossil.

But, new evidence or not, Blast probably won't. (Shrug.)

Steviepinhead · 1 December 2005

Oops, forgot the Archaeopteryxlink:

http://www.msnbc.msn.com/id/10283203/.

And, note, for all of those who claim that PT's tone can at times be too harsh, that I said nothing about bird-brains in the prior post...

'Rev Dr' Lenny Flank · 1 December 2005

for all of those who claim that PT's tone can at times be too harsh,

How on earth can one be "too harsh" towards people who want to (1) destroy science and (2) destroy democracy?

Steviepinhead · 1 December 2005

Goodnight, Chet.

Goodnight, David.

Goodnight, Lenny.

Goodnight clocks, and goodnight socks...

BlastfromthePast · 2 December 2005

Oops, forgot the Archaeopteryxlink:

I've already read about it. It seems to make even more of a muddle of bird evolution. From memory, I think they said that it means Archeopteryx is now more likely related to the dromesaurs than to birds. Just more problems for an already problematic area. There was someone who posted a while back on bird lineages who seemed quite knowledgable, maybe he might want to comment if he's out there.

Renier · 2 December 2005

From memory, I recall Creationists like Gish claiming that Archeopteryx was a bird, and nothing else. The new fossil with the toes intact shows it to not be a true bird. I think it is a prime example of a transitional fossil.

Blast wrote:It seems to make even more of a muddle of bird evolution. From memory, I think they said that it means Archeopteryx is now more likely related to the dromesaurs than to birds. Just more problems for an already problematic area.

It's not true at all. It's an outright dishonest lie! The new data strengthens the link to dinosaurs.

But the Thermopolis specimen, discovered in the Solnhoren region of southeastern Germany, clearly shows that Archaeopteryx's first toe extends from the side of its foot, like a human thumb, instead of backwards. The middle toe could be extended, and it had a large claw at its tip. This configuration is similar to some late Jurassic dinosaur families, including the claw-footed Velociraptor and its cousins. As scientists consider Archaeopteryx to be the first known bird, this discovery strengthens the argument that modern birds evolved from dinosaurs.

'Rev Dr' Lenny Flank · 2 December 2005

It seems to make even more of a muddle of bird evolution.

Says the guy who didn't know what _Caudipteryx_ was. Thanks for your, uh, expert opinion, Blast. (snicker) (giggle)