Community

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Secondary function? Are you sure about that? 100%? What was exactly was the primary function of the Appendix that has been lost?

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I can tell based on your labeling of the coccyx as vestigial that you are not a Dr. The coccyx is the anchor point for muscles in your lower extremities. Without it, you would not be able to go potty. If you can’t eliminate waste, you die. Oh darn, there I go off on that irreducible complexity rant again. So sorry. Just couldn’t resist.

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The goosebump reflex is vestigial? How so? It shouldn’t take much deep thinking or prolonged observation on your part to determine an obvious reason for that reaction. What does this reflex do? It causes the skin to pucker up all over the body when it’s cold giving you peaks an valleys on your skin. The net effect is that it reduces the over all area exposed to the cold. Brilliant yes, vestigial, no.

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If natural selection were the cause of all of our organs, there should be millions of them existing in our body right now because there would be no way to shut off their growth.

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Antibiotic resistance is not an example of evolution, where things become more complex.

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It is only an example of change due to intelligently designed intervention.

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Also, is life better for the bacteria’s host if the bacteria becomes drug resistance? Generally no.

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What does antibiotic resistance bacteria demonstrate?

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Original: Alex123

Some things

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Mutation -
-Mutations generating enzymes that confer antibiotic resistance in bacteria – selection by exposure to antibiotics.
-Mutations conferring the ability to used novel substrates (citrate, nylon)

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Selection -
-Generation of diversity through dietary restriction experimentally observed in sticklebacks (see prev answers for references)

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-Morphological changes driven by introduction of a novel predator ( http://www.news.harvard.edu/gazette/2007/09.20/13-lizards.html)

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-Bird beak structure under bmp4 gene control ( http://focus.hms.harvard.edu/2006/090106/genetics.shtml)

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That mutation can create proteins with new function from existing proteins and that these new proteins confer a survival advantage that is visible to the process of natural selection

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ORIGINAL: alex123
Creationists jump up and down, shouting "evolution in crisis”, but when you ask for evidence of this ‘raging dissent’, what do you get? The same tired old ‘paste-ins’ from quote-mine websites; bla bla.

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OK, so let’s see what we have here - First extract - And your point is? This is simply part of the scientific process – take a theory and push it until it falls over. ... Prof. Saunders webpage:- ...Notice that he is not saying that the neo-Darwinist approach is wrong, ...

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Second extract. This is taken so far out of context that I cannot even begin to comment on it – I don’t even know what the article is about (and I suspect you don’t, either!).

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Who is suggesting that selection works that way? I can make your meat grinder from one part (a rasp). Bit by bit I can add parts to make it work better until I get your 17-part grinder. That’s how evolution works – modification and selection.

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I refer you to my earlier answer – ...Only last week was the announcement of the discovery of Odontochelys, a fossil turtle with a partial shell.

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Cut it however you want, the flagellum is not IC because a structure with a reduced number of components still performs a function and can therefore act as an evolutionary precursor. To be IC those reduced components would have to have no function.

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By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box [1996], p. 39)

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Anyone who could see the E.coli flagellum would be pretty amazing because E.coli does not have a flagellum!

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I trust you can offer some references for these sweeping generalisations?

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Falsifiability is the essence of science and that is why ID cannot be one.

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"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case."

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If fossils of morphologically similar organism are not intermediates you have then to explain why these organisms come and go over time in the fossil record. ...of immutability of species.

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I know – it is deplorable. We don’t talk of ‘Einsteinism’ or ‘Maxwellism’, so why use the term ‘Dawinism’?

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Secondly ‘fit to survive’ is only relative to the context of a given environment – an organism ‘fit to survive’ in, say, warm water may not be so fit in cold water....

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If you don’t have enough faith in your own citation to defend it yourself then why did you use it?

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Brilliant? If you have 'peaks and valleys on your skin, surely this creates a larger surface area, not smaller?! Think a little deeper! Far more sensible is a degenerate reflex from an ancestral condition when we had more body hair than we have now - that would explain both the thermal response and the 'fear' reflex.

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Are wisdom teeth vestigial?

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Wisdom teeth are vestigial third molars. In earlier times, when tooth loss in early adulthood was common, an additional molar had the potential to fill in a gap left by the loss of another tooth.

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ORIGINAL: ot4christ

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Are wisdom teeth vestigial?

Not Alex, but according to Wikipedia:

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Wisdom teeth are vestigial third molars. In earlier times, when tooth loss in early adulthood was common, an additional molar had the potential to fill in a gap left by the loss of another tooth.

I would argue that they are not vestigial and although tooth loss is not as common, it still happens. I still have my lower wisdom teeth, just in case:)

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quote: Jhud

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Mutation -
-Mutations generating enzymes that confer antibiotic resistance in bacteria – selection by exposure to antibiotics.
-Mutations conferring the ability to used novel substrates (citrate, nylon)

While a single point mutation can certainly modify the function of proteins produced, more often than not what we see in the case of resistance and novel dietary sources is a modification of the expression of already extant genes leading to novel results.

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Except this study doesn’t say anything about mutations.

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Well, again, no mutations mentioned;

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In fact, that is the case with most of the examples you posted previously (which you seem not to investigate very closely when you post).

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Much of this is evidence of what is becoming increasingly obvious – that the difference in living organisms aren’t the product of incidental mutations being acted upon by selective factors, but the various expression of common genes, genes which can be silenced or expressed in a variety of ways – but the same genes, apparently extant perhaps since the origin of life itself.

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There are no examples where mutations create what we see happening in life’s development; the development of novel structures, systems, abilities, and body plans.

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GHitch quote:

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Creationists jump up and down, shouting "evolution in crisis”, but when you ask for evidence of this ‘raging dissent’, what do you get? The same tired old ‘paste-ins’ from quote-mine websites; bla bla.

So I suppose you can demonstrate the quote in context says something completely different ? Ok, go for it.

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Darwinists are now terrified of quoting anything for fear of being accused of the ubiquitous and terrible 'quote mining' sin. That's why they rarely quote anything anymore.

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We are constantly barraged by "There is no controversy.” “There should be no controversy.” “It’s okay to expel those who pretend that there is a controversy.” “Academic freedom does not apply where the scientific consensus says there is no controversy.” … --- all of which prove there is!

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Forget quotes if you please,

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look at the facts. You're here disputing.

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New laws are being passed in various states,

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a ton of literature has been published on the non existent controversy

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NS is being described as a failing mechanism for explaining the levels of complexity discovered

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ID is constantly being mentioned in all the main sci mags

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- always the hat tip to Darwin no matter foolish - and always in negative light - but then why?

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You're simple very very mistaken. TO, PT and all the others have taken on ID - if it were insignificant and there such a low level of discontent with the "modern synthesis" no such thing would occur.

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Sadly, this fear of quote mining has led you to respond to ALL quotes as being mined and out of context - so wrong it isn't funny.

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Second extract. This is taken so far out of context that I cannot even begin to comment on it – I don’t even know what the article is about (and I suspect you don’t, either!).

You are way off here. That quote is the actual 'abstract' or summary of the whole article!

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Who is suggesting that selection works that way? I can make your meat grinder from one part (a rasp). Bit by bit I can add parts to make it work better until I get your 17-part grinder. That’s how evolution works – modification and selection.

That's not how machines work. Re-read Peterman's take. You cannot just add parts to your rasp! You have to stop and start over again!

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So rather than “All known diseases are caused by mutations”, you mean “some mutations are associated with diseases”? Better?

Way off again, but that's partly my fault since I did not define the term 'disease' a 'sickness' is not the same as a disease in my sense - I mean disease: as per cancer, MS, MD, SCA, etc etc. A common flu is a sickness but not a disease.

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Thus ALL known diseases and syndromes are associated with mutations.

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If everything is a transitional then nothing can be proven in Darwinism since there exist no partial forms! No nonfunctional, badly adapted forms in the record!

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You don't get what IC is. So before we go any further :

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin's Black Box [1996], p. 39)

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Anyone who could see the E.coli flagellum would be pretty amazing because E.coli does not have a flagellum!

Really?
"In the eubacterial system, the best studied flagella are those of E. coli and S. typhimurium, and I'll briefly outline the structure of these as the "canonical" eubacterial flagella (but see below)." from http://www.health.adelaide.edu.au/Pharm/Musgrave/essays/flagella.htm

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It survives because it is fit - is fit because it survives.

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If fossils of morphologically similar organism are not intermediates you have then to explain why these organisms come and go over time in the fossil record.

No one believes in the immutability of species. IDists point to the Cambrian and Avalonian explosions. Sudden appearance of complete well adapted forms with no viable predecessors.

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The whole strata/geo-time concept is based on geo uniformitarianism. A concept now in considerable trouble.

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I know – it is deplorable. We don’t talk of ‘Einsteinism’ or ‘Maxwellism’, so why use the term ‘Dawinism’?

Why do we use Lamarckism, Calvinism, Uniformitarianism, ....

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How is that malaria, for example, has had more reproductive events every year for the last 100,000 years than mammals have had in their entire existence.

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Yet viruses have supposedly given mammals the genes to become
echo-locating bats, explosion spewing beetles, spider-web modifying wasps and nuclear weapons making humans,

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while malaria is still a life sucking plasmodium that can’t reproduce below 60 deg. Fahrenheit

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Any way, air is a great insulator.

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And why do you wear clothes anyways? Clothes are a Jewish/Christian invention.

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OK, tell you what, why don’t you provide a reference to support your opinion that most resistance in bacteria results from changes in the expression of existing genes rather than their mutation and in return you can have this reference http://www.genetics.org/cgi/content/abstract/163/4/1237 describing the in vitro emergence of cefepime resistance, this reference http://www.badscience.net/2008/06/all-time-classic-creationist-pwnage/ describing the exchange of emails between Lenski and Schafly over the in vitro emergence of the Cit+ enzyme and this reference http://aem.asm.org/cgi/reprint/61/5/2020.pdf#search=%22Irfan%20nylon%20Pseudomonas%22 describing the emergence of the nylonase enzyme (please, please tell me that bacteria were created with the information to generate a nylonase enzyme on the offchance that human beings would someday create nylon!).

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Hmm. Unlike you, course, who seems to have lots of opinions which you do not (cannot?) support with references to scientific investigation?

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So, do you have any references to support your opinion that ancestral species had complete genetic ‘tool-boxes’ that allowed them to diversify to the extent that we see today, or is it just that, your opinion? Because I can provide evidence that this is not the case. Two examples to start with:

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1 – the sequential emergence of complex structure in the fossil record – it took some 150 million years for vertebrates to leave the water and another 50 my to develop flight; it took over 200my fir the first land plants to develop flowers. Why these huge delays in the sequence of appearance if there was a single act of creation with all possible genetic material present from the start?

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2 - functional redundancy in eukaryotic respiratory enzymes – if species do not originate from common ancestors, why are there so many interchangeable versions of cytochrome c, for example, and why do the genes that code for these different versions of cytochrome c show clear phylogenetic relationships when compared across taxa? ( http://www.indiana.edu/~ensiweb/lessons/molb.nu.pdf)

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No, that’s right, these were examples of selection generating diversity. That’s why I put them under the heading of ‘selection’, you see, not ‘mutation’. I thought that if I did that it might avoid confusion -evidently not!

(BTW, there is a lot of very interesting research suggesting that mutations in the Pitx1 control gene are responsible for major morphological changes in sticklebacks, but since it is only wild speculation fueled by irrational Darwinist supposition, I thought I’d better not mention it).

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Plenty of evidence emerging that mutations in control genes has resulted in the emergence of and modification of complex structure. Here are 3 examples:-

http://www.genestocellsonline.org/cgi/reprint/1/1/11.pdf (evidence for homologous pax-6 genes controlling eye development on many diverse taxa),

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http://www.biozentrum.unibas.ch/report0607/gehring.pdf (evidence that the evolution of the Hox-6 gene accounts for the evolution of halteres in dipteran insects from 4-winged ancestors and six-legged insects from multi-legged ancestors) and

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http://www.bio-medicine.org/biology-news/Same-mutation-aided-evolution-in-many-fish-species--Stanford-study-finds-192-1/ (mutation accounting for the evolution of light-armoured freshwater sticklebacks from heavy-armoured marine sticklebacks)

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ORIGINAL: alex123
So I suppose you can demonstrate the quote in context says something completely different ? Ok, go for it.
No problem. Give me the complete articles for context and I will.

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The suggestion that there is a fundamental flaw in the principles of evolution from a common ancestor is generated externally by self-interested creationist groups, not internally by scientists who actually do the work.

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Because of attempts by partisan groups to force religious doctrine into science

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by whom? DI? AiG? RAE?

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It occurs, as I have said before, because of concerted attempts by creationist groups and proponents of ID (‘creationists in suits’) to force their doctrines into mainstream science.

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It is interesting that they have chosen evolution and astronomy as their twin targets, as opposed to any other science.

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You do not see articles denouncing electromagnetic theory in creationist literature – why should this be? Unless, perhaps, it is that evolution and astronomy directly contradict the Genesis account of the origins of the universe, where EM does not?

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You are way off here. That quote is the actual 'abstract' or summary of the whole article! If you say so.

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Not so. Here’s a little thought experiment. I take a rasp (1 part); attach it to a clamp so 0that I have both hands free (2 parts); attach a dish to catch the scrapings (3 parts); add a clip to hold the meat (4 parts); attach the clip to a wheel so I can rotate the meat (5 parts)… I think you see where this is going. At no time have I had to stop and start again. Now, if I remove the rasp from my 5-part assembly the machine stops working, but it doesn’t invalidate the process construction by successive modification.

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And, with all due respect to Mr Petermann (who is probably a very nice man who I would like if I met at a party), he is not a biologist.

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His comments are firmly rooted in an out-dated 19th century mechanistic view of cells as

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False logic. All genetic disease might be caused by mutation, but not all mutations cause genetic disease.

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The fact that a complex structure fails when a vital component is removed does not mean that it cannot have been constructed by the step-wise addition of parts. The only proviso is that these parts have to be added in a sensible order – see my step-wise meat-grinder example above. That means that no structure can be truly IC if you can demonstrate that it has a functional precursor.

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So, what evidence do you have for intelligent intervention at the beginning of the Cambrian?

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Because these are doctrines, not sciences.

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What is a ‘reproductive event’? How many ‘reproductive events is that? ....

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And your point is what?

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It has been a surprise to learn how thoroughly cells process themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. By virtue of their proofreading and repair systems, living cells are not the passive victims of the random forces of chemistry and physics. They devote large resources to suppressing random genetic variation and have the capacity to set the level of background localized mutability by adjusting the activity of their systems."

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"the largest stumbling block in bridging the gap between non-living and living still remains. All living cells are controlled by information stored in DNA, which is transcribed in RNA and then made into protein. This is a very complicated system and each of these three molecules requires the other two- either to put it together or to help it work. DNA, for example, carries information but cannot put that information to use, or even copy itself without the help of RNA and protein. "

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"There is no agreement on the extent to which metabolism could develop independently of a genetic material. In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously - and every reason to believe they cannot. The problem of achieving sufficient specificity, whether in aqueous solution or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible."

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"To some degree the theory has been protected from criticism by a device more common to religion than science: dissent, or merely the discovery of a discordant fact, is a punishable offense, a heresy that might easily lead to professional ostracism...."

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A natural and fundamental question to ask on learning of these incredibly, intricately interlocking pieces of software and hardware is : 'How did they ever get started in the first place?"

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"This genetic lexicon goes back a long long way. Not an iota seems to have changed over 2 billion years; all living beings on earth from bacteria to humans use the same 64 word code"

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"Suppose the actual structure of the DNA molecule were due to to the fact that the bindings of it's bases were much stronger than the bindings would be be for any other distribution of bases, then such a DNA molecule would have noe information content. It's code-like character would be effaced by an overwhelming redundancy... Whatever may be the origin of a DAN configuration, it can function as a code only if it's order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words on a printed page."

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In the first case you linked to a brief abstract about the development of cefepime resistance in certain bacterium. Loike most abstracts it is short on detail, so we don't really know why the resistance developed.

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The alteration of specificity is of particular interest - this fits Behe's 'break to save it' concept. What happens is the molecular structures which control the specific substrate of nutrient the bacterium can utilize is altered so it is more generalized, and bacterium is less limited in what it can 'eat'.

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A good analogy to this is what happens when a governor on a vehicle fails. When I was a teenager, my brother got a 'Moped' which in those days were limited by a governor to about 30mph. My brother however rode the thing like a dirt bike, and eventually wore the governor out, allowing the bike to go at a significantly faster rate. Now the bike didn't 'evolve' a new capability, it lost the ability to limit the speed at which it was driven.

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The same thing is happening with these bacterium; the enzymes that control the specific nutrients they can utilize have been broken, and so the bacteria is free to utilize xenobiotic compounds. This doesn't demonstrate the development of a 'novel' capability.

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So, do you have any references to support your opinion that ancestral species had complete genetic ‘tool-boxes’ that allowed them to diversify to the extent that we see today, or is it just that, your opinion? Because I can provide evidence that this is not the case. Two examples to start with:

Here is an excellent paper published in the journal Cell Cycle - Universal Genome in the Origin of Metazoa

As evidence Michael Sherman cites the following:
<snip quotation>

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1 – the sequential emergence of complex structure in the fossil record – it took some 150 million years for vertebrates to leave the water and another 50 my to develop flight; it took over 200my for the first land plants to develop flowers. Why these huge delays in the sequence of appearance if there was a single act of creation with all possible genetic material present from the start?

Touched on above.

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2 - functional redundancy in eukaryotic respiratory enzymes – if species do not originate from common ancestors, why are there so many interchangeable versions of cytochrome c, for example, and why do the genes that code for these different versions of cytochrome c show clear phylogenetic relationships when compared across taxa? ( http://www.indiana.edu/~ensiweb/lessons/molb.nu.pdf)

Well function redundancy doesn't negate the universal genome, it advances it - redundancy in base forms allows for greater diversity over time, a highly anticipatory condition.

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Plenty of evidence emerging that mutations in control genes has resulted in the emergence of and modification of complex structure. Here are 3 examples:-

http://www.genestocellsonline.org/cgi/reprint/1/1/11.pdf (evidence for homologous pax-6 genes controlling eye development on many diverse taxa),

This link didn't work, which again reminds me of why I don't particularly like discussion via link.

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http://www.biozentrum.unibas.ch/report0607/gehring.pdf (evidence that the evolution of the Hox-6 gene accounts for the evolution of halteres in dipteran insects from 4-winged ancestors and six-legged insects from multi-legged ancestors) and

Actually, this is a great example of what I am talking about - from the paper:
Loss-of-function mutations in Ultrabithorax (Ubx) lead to the transformation of halteres into wings, back to the ground state, whereas gain-of function mutations lead to the transformation of wings into halteres (away from the ground state).

What is being described there is a genetic switch - it turns functionaility on and off, and not only that, the it switches between two different states, both of which are beneficial depending on the need. And this is the product, as noted in the beginning the paper from:

"master control genes which have been highly conserved during evolution" - that is, the information is ancient, and has resisted incidental modification, it is not the result of it.

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http://www.bio-medicine.org/biology-news/Same-mutation-aided-evolution-in-many-fish-species--Stanford-study-finds-192-1/ (mutation accounting for the evolution of light-armoured freshwater sticklebacks from heavy-armoured marine sticklebacks)

Again here we are talking about a genetic switch:

The striking similarity is that in both studies evolution turned to the same genetic switch to work a visible change in the fish. However, in the fin study the group wasn't able to pinpoint the exact genetic alteration.

Basically a control gene is switched on and off determing the expression of the gene which produces armor. Notable is the fact that this effect has been repeated in various stickleback populations, and so isn't at all incidental, but part of the genetic packeage that exists in sticklebacks.

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So none of these examples advance your propositions, and they support what I said previously.

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So I suppose you can demonstrate the quote in context says something completely different ? Ok, go for it.

No problem. Give me the complete articles for context and I will.

In other words your accusation of out of context quoting is based on your imagination.

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The suggestion that there is a fundamental flaw in the principles of evolution from a common ancestor is generated externally by self-interested creationist groups, not internally by scientists who actually do the work.

More NDE obligatory propaganda you've swallowed whole. But there's obviously no use in pointing out the facts to you since you "believe"!

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<snip> promote atheism in the name of 'science' which they only understand as methodological naturalism - a metaphysical construct, not a scientific one.

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by whom? DI? AiG? RAE?

You're kidding right? I guess not. Get your haed out of the sand. I meant, Science, Nature, National Geographic, Nova, Discovery....

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There is indeed a deep seated fear of ID, not because it is "not science" but because it is but they refuse to admit it - so they invent the religious connection

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You do not see articles denouncing electromagnetic theory in creationist literature – why should this be? Unless, perhaps, it is that evolution and astronomy directly contradict the Genesis account of the origins of the universe, where EM does not?

Your logic here is poor to say the best. The reason why no one contests other theories is that there is no reason to.

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And it is, contrary to what you pretend to yourself, the materialists who attack the Big Bang because of its metaphysical implications! Get your facts together.

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Not so. Here’s a little thought experiment. <snip>.

Indeed? You've just proven ID as you had to use design to make it!

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Now try doing it blind, unguided and with no purpose! Iow, get a mentally disabled person to do it without them knowing what they're trying to make. This is getting worse and worse.

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And, with all due respect to Mr Petermann (who is probably a very nice man who I would like if I met at a party), he is not a biologist.

Oh please, not that argument again! Like as if no one but PhDs in biology can understand Darwins simple idea!!!

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His comments are firmly rooted in an out-dated 19th century mechanistic view of cells as

You're contradicting yourself again.

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And your notion of presuming into Peterman's knowledge is pure ignorance.

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Now demonstrate to us how bio systems re-organize themselves by chance into sophisticated machines. You must have a lab example in mind, no?

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It has never been demonstrated, only speculated because the machines are already there and no intelligence is allowed.

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False logic. All genetic disease might be caused by mutation, but not all mutations cause genetic disease.

Your fishing here. You changed my words to mean something different than what I said.

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The fact that a complex structure fails when a vital component is removed does not mean that it cannot have been constructed by the step-wise addition of parts. The only proviso is that these parts have to be added in a sensible order – see my step-wise meat-grinder example above. That means that no structure can be truly IC if you can demonstrate that it has a functional precursor.

Once again, this not demonstratable because one must assume beforehand which came first.

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As for the Cambrian being explained - you really ought to stop believing that speculation passes for evidence or fact, not to mention the standard Darwinian scientific-sounding hot air.

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What is a ‘reproductive event’? How many ‘reproductive events is that? ....

A strange response. You don't know what a reproductive event is?! Did you go to school? Did your parents tell bout the birds and bees?

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Why doesn't rm + ns work on p.f. while supposedly having created many novel forms with far less generations in other forms?

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The answer is that there are clear and yes, testable, limits to what RM + NS can do over time.

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And those limits preclude macro-evo.

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DNA is programmed for constancy and stability with limits of adaptability.

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There is not a single grain (let alone mountains) of evidence available for macro-evolution, nor in fact can there be, as many Darwinians themselves claim since it all occurred in the distant past and is thus not observable.

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All the evidence, including that which you refer to here yourself, is of mere micro evo and cannot be blindly extrapolated into macro given the evidence of stability and limits we now know are there.

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Alex that is an opinion of the observed....... Not really facts.

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ORIGINAL: alex123
No problem. Give me the complete articles for context and I will.

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There is often heated debate over details and mechanisms as I have already said but this does not indicate a failure of the fundamental concepts of evolutionary progression from a common ancestor, and to imply that this is the case using edited ‘quotes’ from Gould and Eldridge et al. is, frankly, dishonest.

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ORIGINAL: alex123
You assume that complex structures cannot arise by stepwise mutation/selection process because the absence of any one part causes the entire structure to fail and the organism is not viable without that structure?

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Clearly not, as shown by the progress of technology from the wheel to the jet engine.