Cephalopod development and evolution

Posted 30 July 2007 by

ceph_tease.jpg

People are always arguing about whether primitive apes could have evolved into men, but that one seems obvious to me: of course they did! The resemblances are simply too close, so that questioning it always seems silly. One interesting and more difficult question is how oysters could be related to squid; one's a flat, sessile blob with a hard shell, and the other is a jet-propelled active predator with eyes and tentacles. Any family resemblance is almost completely lost in their long and divergent evolutionary history (although I do notice some unity of flavor among the various molluscs, which makes me wonder if gustatory sampling hasn't received its proper due as a biochemical assay in evaluating phylogeny.)

One way to puzzle out anatomical relationships and make phylogenetic inferences is to study the embryology of the animals. Early development is often fairly well conserved, and the various parts and organization are simpler; I would argue that what's important in the evolution of complex organisms anyway is the process of multicellular assembly, and it's the rules of construction that we have to determine to identify pathways of change. Now a recent paper by Shigeno et al. traces the development of Nautilus and works out how the body plan is established, and the evolutionary pattern becomes apparent.

Continue reading "Cephalopod development and evolution" (on Pharyngula)

63 Comments

mplavcan · 30 July 2007

Indeed, gustatory impression is a perfectly valid character. For example, I believe that phylogenetic analysis of "tastes like chicken" demonstrates that pork beef and lamb are derived, whereas there is a fair chance that dinosaurs tasted like chicken. I am not aware of a published phylogenetic analysis of "tastes like calamari," but perhaps a collaborative proposal to NSF could be worked out involving extensive taste sampling dumped into the latest version of PAUP or perhaps Mesquite?

Henry J · 30 July 2007

So eating sushi can be a scientific experiment? LOL

Henry

ofro · 31 July 2007

I had a friend whose reason for ordering jellyfish in a Japanese restaurant was that he wanted to try another phylum.
(and it didn't taste like chicken)

Gav · 31 July 2007

"Tastes like chicken" has its own Wikipedia page with a couple of relevant links.

What does Nautilus taste like, anybody know?

Henry J · 31 July 2007

Nemo's submarine? Probably tastes like metal. Oh, you may have meant the animal of that name... :D

James Collins · 31 July 2007

'Panda' says:People are always arguing about whether primitive apes could have evolved into men, but that one seems obvious to me: of course they did! The resemblances are simply too close, so that questioning it always seems silly.

Using the 'Panda' logic we should be able to safely assume that a tail, webbed feet, and a snout resembling a duck's bill makes the platypus closely related to a Duck!!!

Resemblance is NOT an way to arrive at who is related to who.

In fact there is NO real scientific way to solve this problem.

The number of chromosomes bounce all over the scale from one type of creature to another. There is NO way to line up the DNA and determine relationship either. It is all pure guesswork, and bad guesswork at that.

Frank J · 31 July 2007

James,

What's your "guesswork"? Do you have any evidence that might suggest that "humans and other apes originated from two or more origin-of-life events" is a better explanation? If so, when do you think the lineages originated? Again, "best guesses" will suffice for now. Mere incredulity towards the prevailing explanation will not.

Glen Davidson · 31 July 2007

Resemblance is NOT an way to arrive at who is related to who. In fact there is NO real scientific way to solve this problem.

Really? Do you have any idea if you're related to your mother and father, aside from the records? Are the courts faulty in deciding paternity cases? Was it all just guesswork when the victims of 9-11 were identified by their DNA, since of course resemblance (of DNA between samples) is no guide to relatedness? Are humans related to each other? How could you possibly know, since we have to suppose so from their resemblances? I asked Paul Nelson the same thing once, and sensibly he didn't answer (he avoids all sorts of questions).

The number of chromosomes bounce all over the scale from one type of creature to another.

Yes, dolt, we have a 23 haploid chromosome count, and apes have 24. And guess what, our "chromosome 2" has genes corresponding to two ape chromosomes. How can that be? I guess it's all just magic, since we have no way of telling if children are related to parents, humans are related to each other, or primates related through a common ancestor. After all, if you accept the evidence that humans are related, it's the same sort of reasoning that leads to the forbidden conclusion that chimps and humans are related. Gee, and we "materialists" dare to say that creationists and IDists are anti-science. And all we have to show in evidence for this charge are people like James Collins who flatly denies the basis of science (roughly, pattern recognition) and those who studiously avoid dealing directly with the implications of pattern recognition in the same way across "categories," as we see with all of the IDists. Absolutely nothing would work if we applied their subjectivism. Not only science and justice would be utterly perverted, the ordinary inferences made by humans in their daily lives would be undercut by their ignorance and deliberate perversions of human knowing. Glen D http://tinyurl.com/2kxyc7

Henry J · 31 July 2007

Re "Resemblance is NOT an way to arrive at who is related to who."

It's not just similar or not similar, it's the degree of similarity.

Humans and chimpanzees have mostly the same parts, made of mostly the same tissue types, in mostly the same arrangement. That's talking about all or at least the vast majority of parts.

The "resemblance" between platypus snout and duck bill is superficial; in most ways they differ as much as any mammal differs from any bird.

Henry

mplavcan · 31 July 2007

James:

This may come as a shock, but your thoughts have occurred to many scientists before, and there is an enormous literature devoted to dealing with these very issues. Furthermore, much of this literature has been devoted to critically (and I mean savagely) questioning and evaluating methods for phylogenetic reconstruction. Yet still, in spite such intense criticism, an overwhelming majority of scientists view the exercise as both scientific and remarkably accurate, meaning that it has survived the assault and even grown. Now clearly you must have some special insight into the issues that the scientific community has overlooked. Apart from bald-faced assertions of ignorance (your platypus example is freshman-high-school-biology-first-day-of-class stuff, assuming that anyone taught this stuff in high school anymore), perhaps you would care to elaborate? I'm dying to hear them. Please. We all await. Fire away.

Mike O'Risal · 31 July 2007

The number of chromosomes bounce all over the scale from one type of creature to another. There is NO way to line up the DNA and determine relationship either. It is all pure guesswork, and bad guesswork at that.

— James Collins
Simply not true. Actually, we can track changes in chromosome numbers through evolutionary history just like any number of other traits. We can also look at genes that have are still transcribed in one organism that has ceased serving a useful function in another (a pseudogene; go ahead and look up information for the psi pseudogene, for example, if you're actually intent on considering data) and make comparison that other data validate, thus creating a useful model And as far as physical traits, we can indeed tell homologous from analogous traits through things like the fossil record and molecular biology. The fact that both whales and fish have similar structures for locomotion doesn't pose a problem, and neither does both a platypus and duck having a bill since the structures look superficially similar but are physiologically quite different because they developed differently during evolutionary history and follow very different developmental pathways in the given animal. Where on earth did you get the idea that we can't "line up" DNA from different chromosomes, anyhow? It's certainly not a problem I've ever heard an investigator bring up. Can you point to a scientific study in which this problem actually occurred? A link would be nice.

J. Biggs · 31 July 2007

James Collins wrote: Using the 'Panda' logic we should be able to safely assume that a tail, webbed feet, and a snout resembling a duck's bill makes the platypus closely related to a Duck!!!
Actually the tail and webbed feet of a platypus in no way resemble a ducks bill. Although the duck and the platypus do have a common ancestor. I think you have a problem discerning the difference between homologous structures and analagous stuctures. Please study up before you make any more daft assertions.

Mike O'Risal · 31 July 2007

Yes, dolt, we have a 23 haploid chromosome count, and apes have 24.

— Glen Davidson
James has an even more fundamental problem with his insistence that chromosome number is a uniquely defining characteristic. By that definition, someone who had Downs Syndrome, or any number of other disorders rooted in aneuploidy, would no longer be considered human at all. I'm not sure what they'd be according to James.

Bond, James Bond · 31 July 2007

Give me a break, similarities are not scientific proof. It is the weakest proof available. Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias. For example, naturalists say that evolution is proven true when we look at the 98.8% similarity between certain segments of the DNA in a Chimpanzee and compare them with the same segments of DNA of a Human. Yet that similarity is not nearly good enough to be considered "conclusive" scientific proof. For starters, preliminary comparisons of the complete genome of chimps and the complete genome of man yield a similarity of only 96%. Dr. Hugh Ross states the similarity may actually be closer to 85% to 90%. Secondarily, at the protein level only 29% of genes code for the exact same amino acid sequences in chimps and humans (Nature, 2005). As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from! Clearly, we must find if the DNA is flexible enough to accommodate any type of mutations happening to it in the first place. This one point of evidence, (The actual flexibility of DNA to any random mutations), must be firmly established, first and foremost, before we can draw any meaningful inferences from the genetic data we gather from organisms!! Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary theory is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are harmful and/or to the life-form having the mutation (Gerrish and Lenski, 1998)! Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is clearly overwhelming, for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

"It is entirely in line with the al nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes accidentally introduced into any artificial mechanism are predominantly harmful to its useful operation" H.J. Muller (Received a Nobel Prize for his work on mutations to DNA)
"But there is no evidence that DNA mutations can provide the sorts of variation needed for evolution... There is no evidence for beneficial mutations at the level of macroevolution, but there is also no evidence at the level of what is commonly regarded as microevolution." Jonathan Wells (PhD. Molecular Biology)

Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter. Since, it is an established fact that at least 999,999 in 1,000,000 of any mutations to DNA will be harmful and/or , then it is also an established fact that there is at least a 999,99930,000,000 to one chance that the monkey will fail to reach man by evolutionary processes. The monkey will hit a end of harmful/fatal mutations that will kill him or severely mutilate him before him. The poor monkey barely even gets out of the evolutionary starting gate before he is crushed by blind chance. This would still be true even if the entire universe were populated with nothing but monkeys to begin with! This number (999,99930,000,000), is fantastically impossible for any hypothetical beneficial mutation to ever overcome! Worse yet for the naturalists, mathematician William Dembski PhD. has worked out the foundational math that shows the mutation/natural selection scenario to be impossible EVEN IF the harmful/fatal rate for mutation to the DNA were only 50%. The naturalist stamps his feet again and says that symbiotic gene transfer, cross-breeding (yes they, desperately, suggested cross-breeding as a solution), gene duplication and multiplication of chromosomes, alternative splicing etc .. etc .. are the reasons for the changes in DNA between humans and apes. They say these things with utmost confidence without even batting an eye. Incredibly, this is done in spite of solid evidences testifying to the contrary. Indeed, even if a hypothetical beneficial mutation to the DNA ever did occur, it would be of absolutely no use for it would be swallowed in a vast ocean of slightly detrimental mutations that would be below the culling power of natural selection!
"The theory of gene duplication in its present form is unable to account for the origin of new genetic information" Ray Bohlin, (PhD. in molecular and cell biology)

"Evolution through random duplications"... While it sounds quite sophisticated and respectable, it does not withstand honest and critical assessment" John C. Sanford (PhD Genetics; inventor of the biolistic "gene gun" process! Holds over 25 patents!)

The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses in complexity any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick (Trifonov, 1989)! No line of computer code ever written by man approaches that level of data compression (poly-functional complexity). Further evidence for the inherent complexity of the DNA is found in a another study. In June 2007, a international team of scientists, named ENCODE, published a study that indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. This "complex interwoven network" throughout the entire DNA code makes the human genome severely poly-constrained to random mutations (Sanford; Genetic Entropy, 2005). This means the DNA code is now much more severely limited in its chance of ever having a hypothetical beneficial mutation since almost the entire DNA code is now proven to be intimately connected to many other parts of the DNA code. Thus even though a random mutation to DNA may be able to change one part of an organism for the better, it is now proven much more likely to harm many other parts of the organism that depend on that one particular part being as it originally was. This "interwoven network" finding is extremely bad news for naturalists!

Naturalists truly believe you can get such staggering complexity of information in the DNA from some process based on blind chance. They cannot seem to fathom that any variation to a basic component in a species is going to require precise modifications to the entire range of interconnected components related to that basic component. NO natural law based on blind chance, would have the wisdom to implement the multitude of precise modifications on the molecular level in order to effect a positive change from one species to another. Only a "vastly superior intelligence" would have the wisdom to know exactly which amino acids in which proteins, which letters in the DNA code and exactly which repositioning of the 25 million nucleosomes (DNA spools) etc .. etc .. would need to be precisely modified to effect a positive change in a species. For men to imagine blind chance has the inherently vast wisdom to create such stunning interrelated complexity is even more foolish than some pagan culture worshipping a stone statue as their god and creator. Even if evolution of man were true, then only God could have made man through evolution. For only He would have the vast wisdom to master the complexity that would be required to accomplish such a thing. Anyone who fails to see this fails to appreciate the truly astonishing interwoven complexity of life at the molecular level. Even though God could have created us through "directed evolution", the fossil record (Lucy fossil proven not ancestral in 2007) and other recent "hard" evidence (Neanderthal mtDNA sequenced and proven "out of human range") indicates God chose to create man as a completely unique and distinct species. But, alas, our naturalistic friend is as blind and deaf as the blind chance he relies on to produce such changes and cannot bring himself to face this truth. Most naturalists I've met, by and large, are undaunted when faced with such overwhelming evidence for Divine Intelligence and are convinced they have conclusive proof for naturalistic evolution somewhere. They will tell us exactly what it is when they find it. The trouble with this line of thinking for naturalists is they will always take small pieces of suggestive evidence and focus on them, to the exclusion of the overriding vast body of conclusive evidence that has already been established. They fail to realize that they are viewing the evidence from the wrong overall perspective to begin with. After listening to their point of view describing (with really big words) some imagined evolutionary pathway on the molecular level, sometimes I think they might just be right. Then when I examine their evidence in detail and find it wanting, I realize they are just good story tellers with small pieces of "suggestive" evidence ignoring the overwhelming weight of "hard" evidence that doesn't fit their naturalistic worldview. Instead of them thinking," WOW look how God accomplishes life on the molecular level," they think" WOW look what , dumb and blind chance accomplished on the molecular level." Naturalists have an all too human tendency to over-emphasize and sometimes even distort the small pieces of suggestive evidence that are taken out of context from the overwhelming body of "conclusive" evidence. This is done just to support their own preconceived philosophical bias of naturalism. This is clearly the practice of very bad science, since they have already decided what the evidence must say prior to their investigation.
I could help them find the conclusive proof for evolution they are so desperately looking for if they would just listen to me. For I know exactly where this conclusive proof for evolution is; it is right there in their own imagination. What really amazes me is that most naturalists are people trained in exacting standards of science. Yet, they are accepting such piddling and weak suggestive evidence in the face of such overwhelming conclusive evidence to begin with. This blatant deception; , dumb, blind chance has the inherent wisdom to produce staggering complexity, is surprisingly powerful in its ability to deceive! That it should ensnare so many supposedly rational men and women is remarkable. Then, again, I have also been easily misled by blatant deception many times in my life, so, maybe it is not that astonishing after all. Maybe it is just a painful and all too human weakness we all share that allows us to be so easily deceived.

GuyeFaux · 31 July 2007

Bond, James Bond,

Based on the similarity of this post to your post some weeks ago, I will conclude that you're an ineducable trolling moron. Is that scientific enough?

Mike O'Risal · 31 July 2007

This "Bond" person doesn't appear to have the slightest clue about how genetics work; lots of red herring garbage in there that entirely ignores... well... pretty much all of science. Good examples of quote mining, though.

raven · 31 July 2007

James the hit and run creo: Give me a break, similarities are not scientific proof. It is the weakest proof available. Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities while ignoring the foundational principle of science (genetic entropy) that contradicts their preconceived philosophical bias.
1. The first three sentences are lies. It goes downhill from there. Similarities are important evidence for any theory, it is strong evidence especially when consistent with other data sets (which it is), and genetic entropy doesn't exist except in Jame's mind. 2. The chances are low that James can even read much less understand all that gibberish and lies. But maybe he can explain genetic entropy and some other imaginary scientific principles. 3. The chances are high that he just cut and pasted that from somewhere else. Which shows that there are at least 2 people totally confused.

Henry J · 31 July 2007

Re "Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. "

Let's see. Five million years or so in each of the two lineages. 30 million base pairs.

30 million base pairs / ( 5 million years * 2 lineages ) = 3 base pairs per year, or about 60 or so per generation.

Average number mutations per generation over the entire genome is over 100, iirc.
(Average within coding regions is between 1 and 2, iirc.)

No contradiction there.

Conclusion: this guy started a multi-page essay without having done the required math.

Henry

fnxtr · 31 July 2007

His creo-teachers measure quantity of work, not quality.

Bev Collins · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory. The genome appears to have been created, and the genes are turned off and on to create different beings, for the most part.

How is it that all of our binary programs have to be created, yet nature miraculously did this all on her own?

My gut feeling tells me that we're missing something here.

Bev Collins · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory. The genome appears to have been created, and the genes are turned off and on to create different beings, for the most part. How is it that all of our binary programs have to be created, yet nature miraculously did this all on her own? My gut feeling tells me that we're missing something here.

Bev Collins · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory. The genome appears to have been created, and the genes are turned off and on to create different beings, for the most part. How is it that all of our binary programs have to be created, yet nature miraculously did this all on her own? My gut feeling tells me that we're missing something here.

Bev Collins · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory. The genome appears to have been created, and the genes are turned off and on to create different beings, for the most part.

How is it that all of our computer binary programs have to be created, yet nature miraculously did this all on her own?

My gut feeling tells me that we're missing something here.

Bev Collins · 1 August 2007

Where are the half species: The in-between species when one species mutates into another species?

Or,if that's not how it happens, when did a dog give birth to a half something else, or whatever?

You know what I mean.

I think my ex is a mutant. I told him I would ask you guys what his chances are of finding another mutant like him.

I read somewhere that they only used DNA from like 37 some women to trace the whole female lineage down to the Eve-mother.

Well, I'm sure they missed at least one other lineage. If you tested the DNA from my ex-mother-inlaw, I know that the findings would be different. How can they be so sure having traced so few ancestral genomes?

Bev Collins · 1 August 2007

Last question:

If my mother-in-law's DNA was sequenced, tested or whatever you call it, and it was found that her DNA did not make her quite human yet, or if it showed that she had mutated just a little past being human, how would I go about donating her to a lab for experimental research? I mean monkeys are mostly human - 93% - right? So, if we can do it to monkeys . . .

Anyone???

Frank J · 1 August 2007

My gut feeling tells me that we're missing something here.

What's missing is this: Theistic evolutionists who believe that life is designed and created clearly state their conclusions of the whats, whens, and hows (proximate causes), and base them on multiple independent lines of evidence. Anti-evolution activists, and the cheerleaders who mindlessly parrot them, in stark contrast, are being increasingly evasive on what their designer did, when, and how, that would make their "theory" qualify as something other than evolution. The evasion has gotten so bad that the only one to offer a hint of what he thought happened instead (Michael Behe) has conceded the entire 4-billion year timeline and common descent to mainstream science, and none of his colleagues have challenged him directly, even if they seem to disagree.

ben · 1 August 2007

My gut feeling tells me that we're missing something here
I don't know if we are missing anything, but you are clearly lacking a basic understanding of the science you're so smugly attacking.

Mike O'Risal · 1 August 2007

Where are the half species: The in-between species when one species mutates into another species?

— Bev Collins
http://www.pbs.org/wgbh/evolution/library/05/2/l_052_05.htmlThey're right here. They're not even fossils; all the intermediates between the two end species are still very much alive. This is just one example, of course. Ever been to the Grand Canyon? Check out the squirrels there sometime... but you have to go all the way around.

I read somewhere that they only used DNA from like 37 some women to trace the whole female lineage down to the Eve-mother.

— Bev Collins
I don't know what you've read or where you read it, but this isn't what the so-called "Eve hypothesis" is. Mitochondrial DNA, which is passed on only from mother to offspring (has nothing to do with father and is recombined during sexual reproduction like nuclear DNA) was examined from women selected randomly from georgraphically and ethnically diverse populations around the planet. Because mitochondrial DNA changes so slowly over time, comparative analysis allows the construction of phylogenetic trees that are rooted not in a single individual, but in a single population with a minimum size of ~10,000. "Eve-mother" is a misnomer based on popular reporting of a study which most people haven't read and, unfortunately, aren't equipped educationally to understand even if they did. "Eve" sounds better and sells more magazines than "an African population of at least 10,000 individuals that existed in the prehistoric past."

If you tested the DNA from my ex-mother-inlaw, I know that the findings would be different. How can they be so sure having traced so few ancestral genomes?

— Bev Collins
I can't say anything about your ex-mother-in-law; I'm fairly certain my own is descended from wild boars. We can have this certainty because, again, the study didn't look at nuclear DNA, which is prone to a relatively high right of mutation (replicative error) due to the way in which genetic material is parsed out as the result of sexual meiosis; mitochondria are effectively asexual reproducers with a comparatively small genome and don't undergo much mutation and no recombination whatsoever. Because the rate of change is so small and so constant, the mitochondrial genome makes an excellent clock, and we can get a very good idea of how long it takes to go from one sequence to another with a very high degree of predictability. That's not to say that we can get 100% accuracy, but we can definitely make a prediction that allows us to incorporate the small margin of error that does exist (hence "a population of 10,000 individuals" instead of "Bob and Sally Robustus from Kinshasa").

Mike O'Risal · 1 August 2007

Where are the half species: The in-between species when one species mutates into another species?

— Bev Collins
They're right here. They're not even fossils; all the intermediates between the two end species are still very much alive. This is just one example, of course. Ever been to the Grand Canyon? Check out the squirrels there sometime... but you have to go all the way around.

I read somewhere that they only used DNA from like 37 some women to trace the whole female lineage down to the Eve-mother.

— Bev Collins
I don't know what you've read or where you read it, but this isn't what the so-called "Eve hypothesis" is. Mitochondrial DNA, which is passed on only from mother to offspring (has nothing to do with father and is recombined during sexual reproduction like nuclear DNA) was examined from women selected randomly from georgraphically and ethnically diverse populations around the planet. Because mitochondrial DNA changes so slowly over time, comparative analysis allows the construction of phylogenetic trees that are rooted not in a single individual, but in a single population with a minimum size of ~10,000. "Eve-mother" is a misnomer based on popular reporting of a study which most people haven't read and, unfortunately, aren't equipped educationally to understand even if they did. "Eve" sounds better and sells more magazines than "an African population of at least 10,000 individuals that existed in the prehistoric past."

If you tested the DNA from my ex-mother-inlaw, I know that the findings would be different. How can they be so sure having traced so few ancestral genomes?

— Bev Collins
I can't say anything about your ex-mother-in-law; I'm fairly certain my own is descended from wild boars. We can have this certainty because, again, the study didn't look at nuclear DNA, which is prone to a relatively high right of mutation (replicative error) due to the way in which genetic material is parsed out as the result of sexual meiosis; mitochondria are effectively asexual reproducers with a comparatively small genome and don't undergo much mutation and no recombination whatsoever. Because the rate of change is so small and so constant, the mitochondrial genome makes an excellent clock, and we can get a very good idea of how long it takes to go from one sequence to another with a very high degree of predictability. That's not to say that we can get 100% accuracy, but we can definitely make a prediction that allows us to incorporate the small margin of error that does exist (hence "a population of 10,000 individuals" instead of "Bob and Sally Robustus from Kinshasa").

raven · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory. The genome appears to have been created, and the genes are turned off and on to create different beings, for the most part.
That is a false statement. They have done no such thing. The function of noncoding DNA is mostly unknown. The provisional answer right now, some is regulatory, some is just there. It will take decades for scientists to understand noncoding DNA well. This will be done by scientists with lots of hard work. It will not be done by creationists who load up the ABI 1200 LIE SYNTHESIZER and go out for a cup of coffee and call it done. For extra credit, why don't you explain what the 8% of the genome that dates in part back to the monkeys that is defective retroviruses is doing? If a miracle in your soul occurs, explain your activities? "If I post lies on message boards, god exists." Of course, quote from the bible. Avoid the part about 10 commandments.

Richard Simons · 1 August 2007

Regarding Bev Collins's comments: why do creationists persist in thinking that the theory of evolution proposes that speciation occurs over two or three generations? Of course, if that were actually the case, we'd be dealing with creation, not evolution.

To Bev: What exactly do you mean by a 'half-species'? I think if you try to describe this concept in detail you would realize it does not make much sense. To find a 'half-species' between a herring gull and a lesser black-backed gull (both of which breed around the coast of the UK) try travelling around the world and studying the gulls of the Breing Straits and northern Siberia.

raven · 1 August 2007

Where are the half species: The in-between species when one species mutates into another species?
Everywhere. Open your eyes. 1. In a narrow sense, the 1/2 species, 3/4 species, 99% species etc. would be considered subspecies. Many examples, European mice from madeira and Tunisia would be considered species in the making, many ring species, herring gulls, fruit flies. Quite a few cryptic species are being found. Dogs, cats, corn. 2. Many of them are dead and fossilized. For the last common ancestor of chimpanzees/human to human transition, read national geographic or watch Nova. They are in Africa and Eurasia and people dig them up all the time. 3. In a broader sense all fossils are transitional and all extant organisms are transitional. We all came from somewhere and are going somewhere.

Glen Davidson · 1 August 2007

They have recently ascertained that about 95% of DNA is regulatory.

No they haven't. Why don't you go off and learn something, before showing what an ignorant troll you are?

The genome appears to have been created,

What evidence have you for that? You just repeat ancient lies. The genome appears to have evolved, jerk. Deal with the similarites, and then you might be worth listening to.

and the genes are turned off and on to create different beings, for the most part.

They're translated or not, for anyone who cares about the actual details. You're just operating from the mindless tripe your IDiot teachers told you.

How is it that all of our computer binary programs have to be created,

Because they don't reproduce, can't evolve, and are intended to produce the rational results that evolution never produced. If we're just computers, tell me this, why did we need to invent computers to do so much that we cannot do?

yet nature miraculously did this all on her own?

"Miraculously" is your claim, not ours, dimwitted buffoon. You need to learn what evolution entails.

My gut feeling tells me that we're missing something here.

Since all that you have is about as intelligent as the contents of your gut, I think you came closer to the truth than you intended to do. Glen D http://tinyurl.com/2kxyc7

Glen Davidson · 1 August 2007

Where are the half species: The in-between species when one species mutates into another species?

The question of speciation remains. Nevertheless, so-called "half-species" are well attested in certain fossil records. It's just not that interesting aspect for the broad picture of evolution (nor the issue most disputed by idiot trolls like yourself), hence we pay more attention to the half-dinosaur/half-bird fossils like archaeopteryx, and the various hominin transitionals. You know, like H. erectus, our most immediate ancestral species.

Or,if that's not how it happens, when did a dog give birth to a half something else, or whatever?

A little learning wouldn't hurt, you know. We can't make up for your vast deficit, but you could start by looking up "evolution," "transitionals," and "speciation," for instance, on Wikipedia.

You know what I mean.

You mean that you know nothing about what you're criticizing. It comes through loud and clear.

I think my ex is a mutant. I told him I would ask you guys what his chances are of finding another mutant like him.

Looks like he already did, and improved his lot since then.

I read somewhere that they only used DNA from like 37 some women to trace the whole female lineage down to the Eve-mother.

Why don't you do the statistics and tell us how many were necessary?

Well, I'm sure they missed at least one other lineage. If you tested the DNA from my ex-mother-inlaw, I know that the findings would be different. How can they be so sure having traced so few ancestral genomes?

Many weren't sure, but the results have held up. Why don't you try to find some information regarding these matters, instead of throwing the full force of your ignorance at everything? Glen D http://tinyurl.com/2kxyc7

Glen Davidson · 1 August 2007

"Bond" always writes stupidly, without a glimmer of scientific knowledge. Others have hit at his recent bilge, but a bit more comment about the tiny bit I read could be worth another stab:

Give me a break, similarities are not scientific proof.

Nothing is "scientific proof," ignorant troll. Similarities are, however, what provide a huge amount of the accumulated scientific evidence, or indeed, in one sense repetition can be considered to be the aspect of any real evidence that makes it scientific.

It is the weakest proof available.

Not that you'd know anything about it, but Hume already dealt with this. So we know that similarity isn't proof in the least. However, we have shown it to be meaningful, which is why statistics involving similarities can be said to be "meaningful" when they meet certain levels of regularity or "similarity". Perhaps it is time that you learn that science relies heavily upon statistics, which is all about similarity. Indeed, similarity is what is behind anything that is "scientifically meaningful". Only stupid trolls like you would claim that the very basis of science is the weakest "proof", in your mangled English and complete idiocy.

Naturalists always try to establish scientific validity for evolution by pointing to suggestive similarities

Everyone tries to establish scientific soundness by pointing to similarity and to dissimilarity, in the courts and in science, even if they are non-realists or phenomenologists. To bring up "naturalists" is to misunderstand science, but then that's all you do, cretin.

while ignoring the foundational principle of science (genetic entropy)

Little retarded boy, not only could not "genetic entropy" be the foundational principle for, say, orbital mechanics or general relativity for the most obvious (obvious to non-stupid persons) reasons, it isn't a principle at all. It's just a trivial lie that morons like you tell. What is more, imbecile, if it to be of any worth at all it would have to be established by statistical similarities under differing conditions. That is to say, you'd have to show similarities if it were to become a "principle" or anything like scientific, and one would also have to explain how such a "principle" could co-exist with the similarities found across all of life. And you don't even understand what I'm writing about, ignoramus.

that contradicts their preconceived philosophical bias.

Since that "principle" is an unestablished lie which serves only your preconceived nonsense, it's obvious that you're projecting.

You can't even write out the situation properly, can you lackwit? I won't correct your many errors in just that sentence, since you wouldn't understand the corrections anyway. Evolution predicts any number of things, including genetic relatedness where morphological relatedness was inferred. Creationists once denied that this prediction was fulfilled, because they knew very well that if it were not, evolution would not be supported by the overall evidence. Tell me this, fuckwit: What are the chances that unrelated animals would have 95%+ similarity with humans? The chance is practically indistinguishable from zero.

Yet that similarity is not nearly good enough to be considered "conclusive" scientific proof.

Science is contingent, not something that a dullard such as yourself would know. The similarity between human genomes and chimp genomes is way higher than the level needed to show that the two genomes are related. Just a 10% correspondence between the sequences of genes (above what would be expected by chance) is sufficient to indicate that the two genes are related. We have a much greater similarity between chimp and human genes than that, or than the similarities which indicate to intelligent and educated people that yeast (or bacteria, for instance) and humans share a common ancestor. The fact is that you're such a slow and ignorant mutant that you'd probably deny the relatedness of English and German, since of course the words aren't anything like 95% similar. Any real thinker doesn't come up with such lying objections as you do, but then I guess we've known for a long time that you're nothing but a really stupid troll. Glen D http://tinyurl.com/2kxyc7

J. Biggs · 1 August 2007

James Bond wrote: Even if evolution of man were true, then only God could have made man through evolution.
This one statement you made proves the vacuity of your position. ID/Creationism is not science because in the end it agrees with any set of observations and/or theories used to explain them, including evolution. Since you obviously know this to be the case, why do you continue to rail against science when in the end it all agrees with your position no matter what it says?

J. Biggs · 1 August 2007

James Bond wrote: Man has over 3 billion base pairs of DNA code. Even if there were just a 1% difference of DNA between monkeys and humans, that would still be 30 million base pairs of DNA difference. It is easily shown, mathematically, for it to be fantastically impossible for evolution to ever occur between monkeys and man, or monkeys and anything else for that matter.
Glen Davidson wrote responding to a similar bit of gibberish: Evolution predicts any number of things, including genetic relatedness where morphological relatedness was inferred. Creationists once denied that this prediction was fulfilled, because they knew very well that if it were not, evolution would not be supported by the overall evidence. Tell me this, fuckwit: What are the chances that unrelated animals would have 95%+ similarity with humans? The chance is practically indistinguishable from zero.
Glen is, as usual, absolutely right, however, I might add that even though both numbers are approximately zero, the number that correlates with the probability of genetic relatedness is extremely large when compared to the number that correlates with genetic difference. This makes common descent far more probable in your laughable scenario.

J. Biggs · 1 August 2007

James Bond wrote As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from!
No you dimwit. All these genetic similarities show is that we have common ancestry to all of the organisms you mention not that we are 92% mouse or some such thing. And it is your reasoning that is simpleminded and flawed since you are clearly attacking a strawman.

raven · 1 August 2007

James Bond wrote As well, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we 75% worm? No, of course not!! This type of reasoning is simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from!
Those numbers don't look right. Looks like someone just made them up. Rhesus monkey is 93%. IIRC (big if) mouse is 40%. zebra fish is not 92% for sure. Too busy to look them up right now. There used to be tables of DNA:DNA homologies determined by melting curves scattered around the net but they've gotten lost in the flood of info.

J. Biggs · 1 August 2007

James Bond wrote: Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to DNA that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy.
Certainly, the lactase persistence mutation is not the only human genetic polymorphism that has been found to be beneficial. No, I think that there is also an mutant anti-cholesterol gene that actual scientists recently found in some Italians. There are also others advantageous mutations like malaria resistance in heterozygous sickle-cell and thalassemia genes, and also a polymorphism that make individuals resistant to developing HIV. In fact all biological life is composed entirely of "beneficial mutations" so to speak. Its just that most of them were inherited and they happened individually over a long span of time. The most important thing you need to know is that deleterious mutations aren't propagated, mutations that decrease fitness are propagated to future generations at a lower rate, neutral mutations can not be selected for or against so their rate of transmission is unpredictable and mutations that increase fitness are propagated to future generations at a higher rate. Although I have no idea if any of what I said violates "the principle of genetic entropy".

J. Biggs · 1 August 2007

raven wrote: Those numbers don't look right. Looks like someone just made them up.
I agree, they don't look right, but one could hardly expect more from a dishonest fool like Bond. However, even if Bond's percentages are accurate it doesn't change the fact that he is attacking a strawman.

J. Biggs · 1 August 2007

James Bond wrote: NO natural law based on blind chance, would have the wisdom to implement the multitude of precise modifications on the molecular level in order to effect a positive change from one species to another.
No one here has said any "natural law" was based on blind chance idiot. You obviously have no idea what TOE says or you wold understand that there is no predetermined goal towards humans, only creationists think that.
Only a "vastly superior intelligence" would have the wisdom to know exactly which amino acids in which proteins, which letters in the DNA code and exactly which repositioning of the 25 million nucleosomes (DNA spools) etc .. etc .. would need to be precisely modified to effect a positive change in a species.
Again you assume that evolution has some goal. You dishonestly attack your caricature of evolution and then wonder why people who actually know what TOE says think your full of sh*t.
For men to imagine blind chance has the inherently vast wisdom to create such stunning interrelated complexity is even more foolish than some pagan culture worshipping a stone statue as their god and creator.
You foolishly criticize pagan culture worshiping a stone statue as if your religious practices are somehow more supported by the evidence. And again no one here "imagines blind chance has inherently vast wisdom" you mendacious troll. When Chance & natural law is compared to a deity, and they behave indistinguishably from one another to an outside observer, a reasonable person will recognize that the latter is no longer relevant for it can explain anything and everything(including the opposite of what is observed) where as the former can only explain what is observed.

George Cauldron · 1 August 2007

Let me guess: Bond, Bev, and Collins are all one and the same troll.

J. Biggs · 1 August 2007

George Cauldron wrote: Let me guess: Bond, Bev, and Collins are all one and the same troll.
It certainly wouldn't surprise me, since sock-puppetry seems to be a popular tactic for a few of the creos that post on PT. This is especially so among the really stupid trolls like Bond et. al.

hoary puccoon · 2 August 2007

Bond, James Bond--
I'd like to hear more about genetic entropy. Do you have a book out? If you do, how much does it cost? Was it published by a scholarly press? Do you sell it through university book stores? If not, do you sell it at religious book stores? Do you lecture on genetic entropy? If so, do you advertise your lectures at universities? Do you advertise them at churches? Have you ever had a minister bring his flock to hear you? Did you sell books or other written material? I'm just very interested in creationism and its history of fiscal development, so I'd really like to know.

Frank J · 2 August 2007

Let me guess: Bond, Bev, and Collins are all one and the same troll.

— George Cauldron
Two named James and two named Collins. Using Behe/Dembski math there are four. Funny, though, whenever I ask simple questions about their alternative "theory," they usually disappear. Or at least ignore me and reply to those tho take the bait on their PRATTs.

J. Biggs · 2 August 2007

hoary puccoon wrote: I'd like to hear more about genetic entropy.
Bonds the plagiarist was only parroting John C. Sanford who wrote a book titled Genetic Entropy & the Mystery of the Genome in which he uses a version of the very lame 2nd Law of Thermodynamics argument to claim that evolution could not have occurred. Not surprisingly, none of his claims are published in peer-reviewed scientific literature. I realize you're being sarcastic, but that's where this made-up term came from.

cadbrowser · 2 August 2007

I have been a long time lurker here at The Panda's Thumb. And it never ceases to amaze me how many times these trolls are allowed to spill their vile filth. I mean it's the same crap thats been discusses over and over, and yet the contributers seem to oblige any id/IDiot wiling to make an ass of themselves.

I suggest from here on out, if an I.D.'er, fundie, or christian don't have ANYTHING unique to say...just ignore them.

They obviously don't care about evidence, or truth!

J. Biggs · 2 August 2007

cadbrowser wrote: I suggest from here on out, if an I.D.'er, fundie, or christian don't have ANYTHING unique to say...just ignore them.
Does any ID/Creationist ever have anything unique to say? No, It always comes down to Goddidit and these atheist scientists refuse to acknowledge that God is responsible for all we see, Oh yeah and anything scientists observe that conflicts with my presupposed religious position can not be true. Unlike you, cadbrowser, not every lurker understands that the points creationists make have been refuted over and over. Some have to be shown that creationist arguments have a history separate from science and that what ID/Creationism is attempting to do is primarily political.

hoary puccoon · 2 August 2007

J.Biggs,
Thanks. Wow, another "2nd Law of Thermodynamics Disproves Evolution" argument. It's kinda like finding a new Lawrence Welk item at a garage sale, isn't it? Those suckers don't come along every day.

Raging Bee · 2 August 2007

Give me a break, similarities are not scientific proof. It is the weakest proof available.

Well, so much for the "Life forms are like machines, therefore they're designed" argument. You just sank your own flagship, skippy.

fnxtr · 2 August 2007

Game, set, and match, Bee. Well played.

J. Biggs · 2 August 2007

Raging Bee wrote: Well, so much for the "Life forms are like machines, therefore they're designed" argument. You just sank your own flagship, skippy.
They are screwed either way because if they admit that similarity matters then they have to admit that humans and chimps are much more similar to each other than are humans and things that are designed. If they say similarity is the "weakest proof available" then they sink their whole design analogy. Its a lose/lose situation, but I'm sure they're used to that by now.

Henry J · 2 August 2007

Re "Thanks. Wow, another "2nd Law of Thermodynamics Disproves Evolution" argument."

Besides, if something as firmly supported by evidence as evolution did conflict with a law established in another branch of science, it'd be more likely that said "law" would be revised (or restricted as to what situations it applies) than that they'd discard the supported explanation. (Esp. if typing on a keyboard actually did violate it... ;) )

Henry

hoary puccoon · 3 August 2007

Actually, Henry, the 'hard' sciences have a long, sad history of sneering at evolutionary theory and getting egg on their faces when new data came in, confirming the evolutionists.
It started with the great comparative anatomist Richard Owen and included Lord Kelvin and even Erwin Schrodinger among the physicists. (Schrodinger didn't disbelieve evolution but he thought that cells were full of colloids, which would obey unknown laws of physics, instead of large but chemically normal molecules of protein and nucleaic acid.)
And, of course, the geologists laughed at all the fossil evidence showing the continents had moved around until oceanographers trying to map the ocean floor came up with completely unrelated evidence that, yes, the continents had moved around.
So, in fact, scientists haven't been any less skeptical about evolution than the modern creationists are. The only difference is, when the evidence has gone against the scientists, they've been willing to admit they're wrong.

Frank J · 3 August 2007

They are screwed either way because if they admit that similarity matters then they have to admit that humans and chimps are much more similar to each other than are humans and things that are designed. If they say similarity is the "weakest proof available" then they sink their whole design analogy. Its a lose/lose situation, but I'm sure they're used to that by now.

— J. Biggs
Of course they are used to it. And they have nothing to worry about as long as their intended audience falls for the bait-and-switch. Besides, Behe, if not most of his colleagues, has always admitted that humans and chimps are biologically related. And AIUI, he never made it clear whether that particular transition (humans and chimps from the common ancestor) required a designer's intervention (note how "genus" is in the "maybe" category on his "evolved or designed" list). But while most critics repeat ad nauseum how ID "sneaks in God," or "is creationism," far too few take the time to show people the inconsistencies, double-standards, strawman arguments, quote mining etc. that are the cornerstone of the ID scam.

Torbjörn Larsson, OM · 3 August 2007

... the 'hard' sciences have a long, sad history of sneering at evolutionary theory and getting egg on their faces when new data came in, confirming the evolutionists. It started with the great comparative anatomist Richard Owen and included Lord Kelvin and even Erwin Schrodinger among the physicists.
Agreed. But to nuance the above slightly, while Kelvin had ulterior religious motives he wasn't a fundamentalist nor was he skeptical for no good reasons. At the time were was no better known mechanism for the suns heat than contraction of stellar bodies, which didn't gave enough time for the then known geology or evolution. I think modern cladistic likelihoods would overpower any hard science in a fair comparison. "... the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants.") "... an astronomical degree of combined statistical significance (P << 10-300, ...") So speculative and/or cranky physicists have moved on to question modern neuroscience instead. :-o

Torbjörn Larsson, OM · 3 August 2007

while Kelvin had ulterior religious motives
Oops. While Kelvin may have had ulterior religious motives. (I haven't read the man myself, obviously - it's his stellar model that is well known.)

Glen Davidson · 3 August 2007

But to nuance the above slightly, while Kelvin had ulterior religious motives he wasn't a fundamentalist nor was he skeptical for no good reasons. At the time were was no better known mechanism for the suns heat than contraction of stellar bodies, which didn't gave enough time for the then known geology or evolution.

Good point, yes. But just to add to it, while ol' hoary brings up issues worth chewing upon, I think it's fair to say that most in the "hard scientists" did defer to biologists for the most part. Scientists in general have opposed the various attempts to impose the teaching of creationism, implicitly endorsing the prevailing biological view. Most of puccoon's examples come from the old guard who had not come to terms with the "new paradigm" (I hate using such clicheed terms, but it actually fits in here). And Schroedinger was mostly on the side of evolution, but with some odd ideas (some faulty ones were given to him by a biologist) not only in biology but in science altogether (well, "his cat" for one, since the cat is an observer itself, plus no animate observer is actually required. Then he entertained a kind of "cosmic consciousness," which really makes me think "new age"). He was kind of "new age" in a number of aspects. I don't think that one could find anything but a tiny minority of physicists and other "hard scientists" who disagreed with evolution after, say, 1900. True, we find more IDists (especially cosmological, sometimes biological) among physicists than biologists today, but they are very few, and usually not especially good physicists. Glen D http://tinyurl.com/2kxyc7

Torbjörn Larsson, OM · 3 August 2007

Most of puccoon's examples come from the old guard who had not come to terms with the "new paradigm" (I hate using such clicheed terms, but it actually fits in here).
That is a fitting description, I think. It also ties in with those modern theoretical physicists like Penrose who has not come to terms with the implications of modern neuroscience. No doubt Schrödinger and other early quantum physicists had peculiar views in the modern perspective. The earliest quantum concept was a discretization of states from specific rules. It was not until later that it become apparent that a complex wavefunction gives the effortless combination of discrete and continous states that is the unique character of QM. Similarly the absence of testable predictions that allows different QM interpretations opened up for diverse ideas of observers. I don't think Schrödinger's gedanken experiment with a (perfectly) isolated cat as a non-observer was quaint at the time. The later ideas and studies of decoherence and entanglement happened to clarify why it wouldn't work, and defined monitoring environments/classical systems (observers), at least consistently and hopefully testable.

hoary puccoon · 4 August 2007

Lord Kelvin was quite right to criticize the vague, uniformitarian idea that the earth had always existed. His estimate of the age of the earth was much too low, but not because of his religious views. He didn't know of any energy source that could supply the sun with fuel for billions of years. The discovery of atomic energy, of course, changed his viewpoint.
I doubt that many scientists after 1900 did disagree that evolution occurred. But when the implications of evolutionary theory contradicted the accepted 'paradigms' (sorry) in their own field, they almost invariably shrugged off the evolutionary perspective until they got whupped upside the head with some totally unexpected discovery that showed the evolutionary theorists were right, after all.
I'm not sure this was a bad thing, either. It certainly proves that evolution hasn't enjoyed any special aura of infallibility in the scientific community, as creationists like to claim.

Marek 14 · 5 August 2007

Torbjörn Larsson:

Actually, from what I read, Schrödinger's Cat was an attempt of "reductio ad absurdum" - Schrödinger meant it to illustrate absurdities the Kopenhagen interpretation would lead to. I don't think he ever personally thought that the cat would be a non-observer - but according to some of interpretations back then, it would be.

Torbjörn Larsson, OM · 7 August 2007

Back from the weekend and commenting again FWIW.
Schrödinger meant it to illustrate absurdities the Kopenhagen [sic] interpretation would lead to.
That rings a bell. But formally his gedanken experiment was consistent with the classical Copenhagen interpretation, so while it was absurd it wasn't quaint. :-P