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Author Topic:   Is DNA the TOTAL Instruction Set for a Lifeform?
Elhardt
Junior Member (Idle past 3350 days)
Posts: 13
Joined: 10-27-2007


Message 16 of 70 (536551)
11-23-2009 7:42 PM
Reply to: Message 3 by Dr Jack
10-19-2009 7:19 AM


Response
It's too cumbersome to quote others, but just to answer some points that seemed to be directed at me (or Wells, since I'm quoting him).

Using the assumption that what Wells is saying is correct (and maybe it's not), the reason this could be a problem for the Darwinian mechanism for evolution is because our current theory of evolution is based on DNA mutations and natural selection. According to him, if the developmental plan is not fully specified by the DNA, then mutations to DNA are not enough to produce a new type of animal (or species). Now, as in another post, exactly what a "species" is, is vague. But as usual, it's back to the fruit fly and an example of mutations leading to other fruit flies. Okay, maybe they're another species of fruit flies, but I'm looking for more than that, since obviously the two are going to be nearly identical anyway. I don't think that's what Wells is talking about. How about replacing the DNA of an ape with that of a human? If you don't get a human with an entire set of human DNA, then there must be more that's needed. But I'm being told by some here, that everything outside the DNA that is needed is also specified by the DNA. It's confusing.

Here's something that I've wanted to know because it's related. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

As for somebody asking about my video, I don't know when I will put it out. I'm always busy bouncing around between things, but there is some stuff that needs to get out there because I'm getting a bit fed up with some of the nonsense I'm hearing and a lot of stuff that's being ignored. What I wanted to do first was run some of the stuff by some relatively knowledgeable people, because I'd like to be sure what I say is rather air tight. There are a few things I know will leave people in silence or cause them to become irrational, illogical, and go into denial, all of which means they've lost the debate. On another forum I asked for a Darwinian explanation for an observation made by Alfred Wallace which ended up that way, and no Darwinian explanation was provided, nor would it be expected that anybody ever could, because it's a failure of a theory to account for all relevant things. And yes, my youtube name is Elhardt.


This message is a reply to:
 Message 3 by Dr Jack, posted 10-19-2009 7:19 AM Dr Jack has responded

Replies to this message:
 Message 17 by Wounded King, posted 11-24-2009 4:29 AM Elhardt has not yet responded
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 Message 19 by deerbreh, posted 11-24-2009 9:25 AM Elhardt has not yet responded
 Message 20 by NosyNed, posted 11-24-2009 2:15 PM Elhardt has not yet responded
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Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 17 of 70 (536579)
11-24-2009 4:29 AM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Re: Response
According to him, if the developmental plan is not fully specified by the DNA, then mutations to DNA are not enough to produce a new type of animal (or species)

This is clearly not the case. Even if the developmental plan is not fully specified by DNA it doesn't follow that changes in DNA are insufficient to produce a new species or sufficient morphological change to constitute a new type of animal. All it would need surely is for the body plan to be substantially specified by the DNA. We know that environmental factors can effect the development of a growing embryo, but we also know that genetic factors can effect embryonic development. One does not preclude the other.

I don't think that's what Wells is talking about.

That is because Wells is constructing a strawman which has little if any relevance to evolution. Evolution does not proceed by a whole human genome suddenly appearing as if by magic in a chimpanzee oocyte. Both the oocyte composition and the genome are changing over the same period of evolution.

If you don't get a human with an entire set of human DNA, then there must be more that's needed.

We've already answered this half a dozen times. The oocytes of different species are different. The composition of those oocytes is not produced by the genetic complement of the embryos, it is rather a product of the maternal DNA. Not everything needed for development is provided by the Oocyte/embryonic DNA, after all at some stage it will need input from its external environment even if it is just gaseous/oxygen exchange. In general the more closely related species are the more likely a nuclear transfer is to succeed in developing to later stages.

It is important to bear in mind that the common technique of Somatic cell nuclear transfer has added barriers in many organisms due to the accumulation of epigenetic modifications to the genome. These modifications such as DNA methylation and histone methylation and acetylation change the dynamics of expression of various genes in the somatic cell and can lead to incompatibilities of the somatic nuclear DNA with the host oocyte, this occurs even in the same species and is why Dolly as a successful example of mammalian SCNT was such a breakthrough.

One good example of an at least partially independent organelle is the mitochondrion, I imagine that Wells prefers cytoplasmic structures and microtubules though since the mitochondrion actually has its own genetic complement, blowing a further hole in Wells's attempts to marginalise the role of DNA. It is worth noting though that the mitochondrion still requires gentic elements in the host cell nuclear genome to function properly and replicate. Except for a handful of cases inheritance of mitochondria is exclusively maternal, another example of the maternal genome determining the composition of the Oocyte, and extended genome included the mitochondrial DNA in this case.

But DNA doesn't hold "shape data" does it?

Not as an interpretable set of 3D coordinates no, but it arguably contains the network of procedural rules for generating the correct 3D structure.

Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified?

This question is of course the entire focus of developmental biology and it is not one that has been fully answered. But as far as we have one the answer is very clearly that the shape is indeed specified by the genome, though obviously it is not stored as any form of "3D geometry data", rather it is stored in a complex network of interacting proteins and enzymes coded for by DNA and the multiple non-coding genetic elements with which they interact. This is clearly seen in the fact that changes in DNA can lead to changes in the skull morphology, exactly the sort of change in developmental endpoint that Well's denies exists. One example of this, not the skull per se, is in the effect of Bone Morphogenetic Protein on the shape of avian beaks (Wu et al., 2006). For a review of elements of cranial skull development and some of what we know about its genetic basis see Opperman (2000).

Sounds like membrane patterns and microtubule arrays according to Wells.

There is absolutely not a scrap of evidence for this, and I'm not even sure Wells goes as far as to make such a specific claim does he?

On another forum I asked for a Darwinian explanation for an observation made by Alfred Wallace which ended up that way, and no Darwinian explanation was provided, nor would it be expected that anybody ever could, because it's a failure of a theory to account for all relevant things.

Maybe you should pose the same conundrum to us in another thread.

TTFN,

WK


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

    
Dr Jack
Member (Idle past 216 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 18 of 70 (536589)
11-24-2009 6:06 AM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Re: Response
Do you really think that's a response, Elhardt? You didn't respond to a single one of the points that have been raised so far, you didn't even respond to the points I made in the post you replied to.

According to him, if the developmental plan is not fully specified by the DNA, then mutations to DNA are not enough to produce a new type of animal (or species)

This is either a) bollocks, or b) sophistry, depending on how you interpret it. It's bollocks for the reasons we've already pointed out several times (i.e. although an egg is not specified by the DNA of the offspring it is specified by the DNA of the mother).

Or it's sophistry because it's trivial true. DNA is not a "plan", it's a chemical; it operates through the action of other chemicals to produce new chemicals. These chemicals interact with each other and the environment in ways that DNA does not specify. The laws of physics do that. True enough but utterly meaningless for the question at hand.

And even if it wasn't a) bollocks, or b) sophistry, it still doesn't follow! It doesn't make any sense to claim that because DNA doesn't 100% describe an organism it can't mutate and evolve - that's like claiming that because the ingredients in a cake don't 100% control how it comes out, you can't make different cakes by changing the ingredients.

Here's something that I've wanted to know because it's related. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

Nothing like learning a bit of biology before you decide you're qualified to criticise it, is there? Or, to quote Ben Goldacre, "it's a bit more complicated than that".

DNA codes for proteins, and which proteins are expressed at which times and under which circumstances. Three dimensional shape is produced by chemical gradients which affect gene expression, and which themselves are formed by the differential timing of gene expression. So, no shape data, but everything that is needed to produce shape.

Edited by Mr Jack, : No reason given.


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

  
deerbreh
Member (Idle past 1004 days)
Posts: 882
Joined: 06-22-2005


Message 19 of 70 (536620)
11-24-2009 9:25 AM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Re: Response
But I'm being told by some here, that everything outside the DNA that is needed is also specified by the DNA. It's confusing.

Well it is only confusing if you are refusing to accept that development is controlled by DNA. The only reason to take such a stance is not understanding the mechanism. But lack of understanding is not a basis for denial of the truth of the matter. There are lots of things I don't understand, for example how come all of the oak trees in a particular location "know" to produce lots and lots of acorns the same year and thus insure that the squirrels will only be able to eat so many and there will be plenty left over for making more oak trees. But that doesn't mean that synchronized mast production isn't under the control of DNA - obviously it is, as all oak trees are closely related in terms of DNA. However DNA is never the whole story. Genes are turned on and off by environmental cues, whether one is talking about trees producing mast or the location and age of a cell in a developing embryo determining whether it will develop into neural tissue or muscle tissue.


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

  
NosyNed
Member
Posts: 8842
From: Canada
Joined: 04-04-2003
Member Rating: 6.7


Message 20 of 70 (536691)
11-24-2009 2:15 PM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Shape Data
. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

You are correct, DNA doesn contain any "shape data". Nor does the recipe for cookies contain any "shape data" but they acquire a pretty specific shape anyway. DNA simply (ha! simple not so much ) describes the chemicals which will be mixed. The results of the chemical reactions produces shapes but the shape isn't specified like it is in a blueprint -- the shape is what emerges when you do the chemistry.


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

  
deerbreh
Member (Idle past 1004 days)
Posts: 882
Joined: 06-22-2005


Message 21 of 70 (537736)
11-30-2009 5:15 PM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Re: Response
Here's something that I've wanted to know because it's related. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

What makes you think that DNA doesn't hold "shape data"? My head looks like my Dad's head - except where it doesn't. Then it looks like my Mom's head. So I have my Dad's forehead, my Mom's jaw and my nose is somewhere in between. I can see the same thing in my daughters. Oldest daughter has my forehead and also over sized head - too bad for her, youngest daughter has my wife's forehead and normal sized head. Obviously DNA does control "shape data". Wells is full of crap.

Note - Just because we cannot necessarily identify WHICH gene or genes control head shape doesn't mean they aren't there. We see the results. Why should shape be any less likely to be under gene control than any other characteristic? Distinct lack of logic here.

Edited by deerbreh, : amplification


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

  
deerbreh
Member (Idle past 1004 days)
Posts: 882
Joined: 06-22-2005


Message 22 of 70 (537738)
11-30-2009 5:25 PM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


Re: Response
Using the assumption that what Wells is saying is correct (and maybe it's not)

Well, DUH....

Isn't that what the argument is about? You really have to do better than that if you want to compete in an argument where sound logic is a requirement. See logical fallacy known as "Begging the Question".

http://en.wikipedia.org/wiki/Begging_the_question


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

  
Briterican
Member (Idle past 2060 days)
Posts: 340
Joined: 05-29-2008


Message 23 of 70 (538514)
12-07-2009 4:35 PM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


DNA acts as a recipe, not a blueprint
Elhardt writes:

Here's something that I've wanted to know because it's related. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

DNA's role in the development of an organism isn't that of a one-to-one blueprint, it is more like a recipe. An embryo develops from bottom-up, localised rules.

Richard Dawkins in "The Greatest Show on Earth" writes:

The beautifully 'designed' body emerges as a consequence of rules being locally obeyed by individual cells, with no reference to anything that could be called an overall global plan.

Edited by Briterican, : No reason given.

Edited by Briterican, : Trimming.


This message is a reply to:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Elhardt has not yet responded

    
Wounded King
Member (Idle past 2206 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 24 of 70 (622036)
06-30-2011 8:32 AM


Bump for ganondorf
I think that this post addresses some of the same issues as were raised in Ganondorf's new topic proposal.

The only specifc example that Dr. Zaid gives on his website as evidence that DNA does not contribute to shape is that he says the deposition of collagen is not controlled by DNA once it has left the cell, and therefore the shape of a developing hand, is largely due to the deposition of collagen as extracellular matrix.

Dr. Zaid writes:

To know the answer to this question we need to understand how genes and DNA work, the genes are part of the information contained in the DNA molecule such that this information when it is read it becomes a protein and proteins are the building blocks of living creatures (like the bricks, glass, and stone comprising a building). The DNA is found only in the nucleus of the cell and as such the controlling action of the DNA is localized within the cell (shown in figure (2) part (A)).

So when the proteins leave the cell (taking the collagen protein as an example) and they are found in the space outside of the cell (shown in figure (2) part (B)), then the big question now is: Can the DNA control the collagen proteins to form the shape of the hand for example (shown in figure (2) part (C))?

The answer is NO, because as we said the control of the DNA is found only within the nucleus of the cell. Thus it can be concluded that genes and DNA can not code (memorize) the design information of a creature and as such design changes occurring in a certain generation of organisms can not be transferred to the next generation using genes and so there is no basis for the evolution claim.

His argument really doesn't make any sense. While DNA may not actively direct the transport of collagen once it has left the cell the distribution of collagen producing cells is governed by different levels of gene expression in response to specific morphogenic signals which are themselves the protein products of DNA.

Apparently Dr. Zaid has never bothered to study anything in the field of developmental biology.

TTFN,

WK

Edited by Wounded King, : No reason given.


Replies to this message:
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Taq
Member
Posts: 7701
Joined: 03-06-2009
Member Rating: 5.4


Message 25 of 70 (622115)
06-30-2011 5:58 PM
Reply to: Message 24 by Wounded King
06-30-2011 8:32 AM


Re: Bump for ganondorf
His argument really doesn't make any sense. While DNA may not actively direct the transport of collagen once it has left the cell the distribution of collagen producing cells is governed by different levels of gene expression in response to specific morphogenic signals which are themselves the protein products of DNA.

Using the same argument, one could say that firefighters are useless for putting out fires because they can not control the water after it has left the hose.


This message is a reply to:
 Message 24 by Wounded King, posted 06-30-2011 8:32 AM Wounded King has not yet responded

  
pandion
Member (Idle past 1111 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 26 of 70 (622273)
07-02-2011 1:16 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


quote:
Developmental Biologist Jonathan Wells...

There's the story right there. Dr. Wells is a moonie who began his studies of biology with the approval and financing of Sun Myung Moon, the leader and founder of the Unification Church. This was after he was awarded a degree by the unification theological seminary and then a PhD in theology from Yale. His expressed purpose in studying evolutionary biology was to learn enough to show that Darwin was wrong. You might suspect that he isn't giving you the straight truth in anything he says. Consider that his purpose it not to present science, but to glorify Sun Myung Moon. He has said so himself. Wells is, in fact, a molecular and cell biologist from UC Berkeley. Wells is the author of Icons of Evolution in which he misrepresents the facts of evolution, all for the glory of Father Moon.
This message is a reply to:
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Replies to this message:
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Taq
Member
Posts: 7701
Joined: 03-06-2009
Member Rating: 5.4


Message 27 of 70 (622287)
07-02-2011 3:17 AM
Reply to: Message 26 by pandion
07-02-2011 1:16 AM


There's the story right there. Dr. Wells is a moonie who began his studies of biology with the approval and financing of Sun Myung Moon, the leader and founder of the Unification Church. This was after he was awarded a degree by the unification theological seminary and then a PhD in theology from Yale. His expressed purpose in studying evolutionary biology was to learn enough to show that Darwin was wrong. You might suspect that he isn't giving you the straight truth in anything he says. Consider that his purpose it not to present science, but to glorify Sun Myung Moon. He has said so himself. Wells is, in fact, a molecular and cell biologist from UC Berkeley. Wells is the author of Icons of Evolution in which he misrepresents the facts of evolution, all for the glory of Father Moon.

No matter what Wells may believe, the fact of the matter is that he only has one poorly written peer review article on his CV. That spells "FAIL" amongst any scientific circle.


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 Message 26 by pandion, posted 07-02-2011 1:16 AM pandion has not yet responded

  
derwood
Member
Posts: 1457
Joined: 12-27-2001


(1)
Message 28 of 70 (625327)
07-22-2011 10:49 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


Wells a biologist?
quote:
Developmental Biologist Jonathan Wells brings up something that seems to be a death blow to the theory (if he's correct) regarding DNA. He says "When an egg's genes are removed and replaced by those of another type of animal, development follows the pattern of the original egg until the embryo dies from the lack of the right proteins"..."Biologists have found that mutations in developmental genes often lead to death or deformity, but they never produce changes that benefit the organism. DNA mutations never alter the endpoint of embryonic development: they can't even change the species".

First, I would point out that Wells is as much a developmental biologist as I am a famous physicist - I took a couple of physics classes, but that doesn't make me a physicist. Wells' sole purpose for obtaining a doctorate was to lend credence to his anti-evolution claims. After more than 10 years in his graduate program, he produced a measely 2 multi-authored papers, on neither of which was he anywhere near first author. If you do not know, most grad programs in the science only require 4-6 years to complete, and most competent students produce 5+ papers in that time.

On to Wells' claim - he is either monumentally ignorant or is simply deceiving his readers whom he hopes are more ignorant than he is and/or will not bother to think his claims through or check his facts.

Prior to removing the nucleus of the zygote, it has been 'directing' the production of growth and development related proteins. Remove the nucleus, insert the nucleus of another, and, just as Wells claims, development proceeds UNTIL the 'right' proteins are used up.

Which means that the internal structure of the zygote and the blastomeres that are produced during those few rounds of cleavage prior to zygote death require the proteins present in the cytoplasm that were produced prior to the manipulation.

If Wells' claims had merit, then the zygote should have kept on going to develop into the 'new' animal.

The remainder of the quote is simply silly and brings up a rather foolish but typical YEC/IDC tendency/trait - you may want to look into the HOX genes first, but note that Wells is essentially claiming that if we do not have the evidence he thinks we should today, then the entire premise is false. This sort of nonsense is a very common creationist rhetorical tool. Johnson used it a lot in his DoT book. Wells is doing it here. That he claims - and you reiterate - that he is a 'developmental biologist', i.e., a scientist, he SHOULD know that such a position is anathema to science and is on top of that, plain silly.

At best, Wells could claim that there is not enough data/evidence to draw a conclusion. But that would not sell books to the faithful, would it?


This message is a reply to:
 Message 1 by Elhardt, posted 10-19-2009 4:25 AM Elhardt has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 29 of 70 (625328)
07-22-2011 10:53 AM
Reply to: Message 16 by Elhardt
11-23-2009 7:42 PM


seen this argument before
Dude - did you ever post on the old CreationTalk forum?

quote:
Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?

There is no 3D geometry data, for none is needed. The geometry comes from the effects of concentration gradients and cell-cell interactions. A basic understanding of developmental biology would allay this fallacy (funny Wells didn't explain this).
This message is a reply to:
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derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 30 of 70 (625329)
07-22-2011 10:56 AM
Reply to: Message 14 by deerbreh
11-17-2009 11:34 AM


Re: Mysterious Centrosomes?
Interestingly, while plant cells do produce centrosomes, they are not made up of centrioles, so the real 'mystery' is why the Designer felt that animal cells would need them.

Edited by derwood, : No reason given.


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