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Author Topic:   Is DNA the TOTAL Instruction Set for a Lifeform?
Elhardt
Junior Member (Idle past 3343 days)
Posts: 13
Joined: 10-27-2007


Message 1 of 70 (531608)
10-19-2009 4:25 AM


I'm slowly gathering facts together for a future video about the Darwinian mechanism for evolution (actually, it's failures), and one topic I wanted to cover seems to be yielding conflicting information. So I want to ask on this forum for any possible clarification or answers.

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".

He goes on about microtubule arrays and membrane patterns in the egg, and how those arrays are created by mysterious organelles called centrosomes which are inherited independently of an organism's DNA. He says "It is quite clear that developmental programs cannot be reduced to genetic programs, written in the language of DNA sequences. It would be more accurate to say that they are written into the structure of the entire fertilized egg---including its DNA, microtubule arrays, and membrane patterns". Basically he's bringing this up to show that this can't be explained by our current theory of evolution. If you can't get from one species of animal to another by replacing or mutating its DNA, then the Darwinian explanation is finished. Also, since all cells have the same DNA, and yet cells differentiate themselves into different types during development, something outside of the cell's DNA has to be in play (microtubule arrays, membrane patterns).

However, when reading about cloning, it was mentioned that cat DNA was put into a rabbit egg, and the outcome was a cat clone. I thought that was impossible based on Wells' description. What am I missing here? Is Wells wrong, or is something else going on in cloning that isn't relevant to what Wells is talking about? I'm confused. If anybody is an expert in this area, please speak up. Thanks.

-Ken Elhardt


Replies to this message:
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AdminModulous
Administrator (Idle past 208 days)
Posts: 897
Joined: 03-02-2006


Message 2 of 70 (531632)
10-19-2009 7:03 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Is DNA the TOTAL Instruction Set for a Lifeform? thread in the Proposed New Topics forum.

Edited by Admin, : Rerender for thread name.


    
Dr Jack
Member (Idle past 209 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(2)
Message 3 of 70 (531635)
10-19-2009 7:19 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


You cannot make an organism simply with the nuclear DNA, it requires the structures of the cell, and the correct environment to develop in order to successfully grow into an adult. DNA on it's own is a relatively inert, uninteresting chemical - it requires a complex set of other chemicals and structures to perform it's array of functions. However (with the important exception of Mitochondria) all the information required to produce these cellular structures and the correct growing environment, etc. is itself in the DNA, it's just enacted by the parent, not the offspring.

One important point to remember when talking about DNA is that while the analogy of an "instruction set" is widely used as a simple way to understand DNA for a non technical audience it is only an analogy and one shouldn't get too wedded to it when trying to understand how DNA actually functions.

How exactly any of this is supposed to pose any kind of a problem for evolution I have no idea?


This message is a reply to:
 Message 1 by Elhardt, posted 10-19-2009 4:25 AM Elhardt has responded

Replies to this message:
 Message 16 by Elhardt, posted 11-23-2009 7:42 PM Dr Jack has responded

  
Modulous
Member (Idle past 208 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(3)
Message 4 of 70 (531648)
10-19-2009 8:47 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


Developmental Biologist Jonathan Wells

I think he once taught embryology at a college once, but I don't think really qualifies him for that title. But that, of course, is an aside.

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".

Did he provide evidence for this claim?

However, when reading about cloning, it was mentioned that cat DNA was put into a rabbit egg, and the outcome was a cat clone. I thought that was impossible based on Wells' description. What am I missing here? Is Wells wrong, or is something else going on in cloning that isn't relevant to what Wells is talking about?

It seems the opposing claim does have evidence. I'd go with the evidence. Wells being wrong sounds like a reasonable conclusion to make, he's often in the position of having the evidence against him.


This message is a reply to:
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Wounded King
Member (Idle past 2199 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(4)
Message 5 of 70 (531653)
10-19-2009 9:15 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


Well's may have done a PhD in developmental biology but I think it is generous to still call him a developmental biologist. He had 2 publications from his PhD research in 1996 and 97 and has only published one thing since, a purely speculative paper about a role for polar ejection forces generated by centrioles in causing cancer which was published in 2005. So it is over a decade since Well's had any published research in the field of developmental biology.

Wells writes:

"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"

Well's is essentially correct here. There are certainly exceptions amongst closely related species, such as the many ongoing experiments to regenerate extinct or threatened species by SCNT into related species, but most highly divergent species will not develop to term in such a case. I certainly don't think that the cat-rabbit experiments you discussed gave rise to full term cat clones.

This is because the oocyte is nothing like identical in many different species. If you compare a human oocyte to a Xenopus you will find they are 1/10th the size and of strikingly different composition with the Xenopus oocyte containing large quantities of yolk proteins for the embryo to feed on.

Wells writes:

"Biologists have found that mutations in developmental genes often lead to death or deformity, but they never produce changes that benefit the organism..."

Well this is a disingenuous argument. By far the vast majority of mutational experiments in developmental biology are done with the explicit purpose of breaking genes to such an extent that they cause death or deformity. This is done because death and deformity are nice readily apparent things which can be easily identified and scored. So most mutational studies are crudely designed to make large severe damaging mutations with ionising radiation or potent mutagenic chemicals.

These experiments are done to elucidate the normal course of devlopment, that is why they are developmental biology experiments. When it comes to looking for beneficial mutations in an experimental setting evolutionary biologists will normally tend to look at microorganisms with generation times measured in hours or days rather than multicellular organisms with generation times in weeks or months.

The only way to identify beneficial mutations is by following the success of various mutations in a population and observing which ones confer improved reproductive success. Obviously this takes several generations to properly establish as you need to exclude the effect of random factors causing genetic drift.

So Well's is technically correct that this hasn't been seen experimentally but neglects to mention that no one is actually doing such experiments to generate beneficial mutations in specifically developmental genes. He assumes such mutations do not exist, but he has no evidence for it. There are examples of beneficial mutations in a number of other types of genes such as metabolic genes allowing for insecticide resistance.

Wells writes:

"DNA mutations never alter the endpoint of embryonic development: they can't even change the species"

Clearly this argument is confused, the various deformities Well's previously mentioned are examples of DNA mutations altering the developmental endpoint. If he means thta we don't see frogs giving birth to cats, well that is evolution as only a creationist could understand it.

He is certainly wrong about changes in DNA not giving rise to new species, although as a creationist his definition of species may be highly idiosyncratic. There are numerous examples from Drosophila of cases where the genetic basis of reproductive isolation, arguably an efffective definiton of distinct species, has been clearly identified.

The genes Nup160 and Nup96 which produce proteins involved in the nuclear pore complex have both been shown to cause hybrid incomaptibilites between D. simulans and D. melanogaster (Presgraves et al., 2003;Tang and Presgraves, 2009).

Anopther such paper on the same species is (Brideau et al., 2006) which is interesting as it again describes hybrid incompatibility between D. simulans and D. melanogaster. In fact the experiments done in the Nup160/Nup96 papers were performed on hybrids which had had the incompatibility caused by the appropriately named Lethal hybrid rescue gene rescued, protecting the hybrid males from their usual fate of death.

So these experiments identified 4 distinct genes with specific mutations combinations of which could produce reproductive isolation but which indivdually did not, therefore allowing the existence of hybrid populations as intermediates between the two distinct species.

He goes on about microtubule arrays and membrane patterns in the egg, and how those arrays are created by mysterious organelles called centrosomes which are inherited independently of an organism's DNA.

Why does he think these are mysterious? This is one of those words like complex which creationists think will magically make their argument for them despite being completely worthless in scientifc terms. Membranes aren't produced by centrosomes, I think either you or Well's misunderstood something. Or does membrane patterns refer to membrane associated feature like the cilia or transmembrane proteins?

In any case as Mr. Jack points out it is incorrent to say these are independent of DNA. They are not all synthesised de novo in the new zygote after fertilisation but they were dependent on a number of proteins coded by DNA for their creation. Obviously this is an example of 'irreducible complexity' in the trivial sense that without one element the other could not exist in its current state, it is considerably harder to show that it is 'irrecudibly complex' in the sense that such a system could not evolve from functional intermediates, indeed cell division in the absence of a centrosome has been shown to occur and indeed the full development of adult flies (Megraw et al., 2001).

Basically he's bringing this up to show that this can't be explained by our current theory of evolution.

This may be why, but it doesn't do that. It certainly shows that DNA is not the be all and end all of development, or evolution, but then no develop mental biologist has held that view for about the last 30 years. Epigenetic factors are readily accepted as a key component in development, indeed one of the major problems with intraspecies, let alone cross species, SCNT is the presence of epigenetic markers which make the DNA distinct from that in a newly fertilised zygote.

If you can't get from one species of animal to another by replacing or mutating its DNA, then the Darwinian explanation is finished.

This seems reasonable, but it also happens to be demonstrable that you can do this in some cases, i.e. the Drosophila species I mentioned previously.

Also, since all cells have the same DNA, and yet cells differentiate themselves into different types during development, something outside of the cell's DNA has to be in play

Absolutely, but in a lot of cases it is simply the products of that cells DNA. The whole way development produces thgese different cell types is not through magical effects of mysterious organelles like the centrosome but through the complex interaction of the whole embryonic environment with the genome.

To act as if this is all a complete mystery is simply to ignore all of the devlopmental research of the last 30-40 years which has been an ongoing process elucidating exactly how differentiation and diversification occur.

TTFN,

WK


This message is a reply to:
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Replies to this message:
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straightree
Member (Idle past 2855 days)
Posts: 57
From: Near Olot, Spain
Joined: 09-26-2008


Message 6 of 70 (535189)
11-13-2009 3:10 PM
Reply to: Message 5 by Wounded King
10-19-2009 9:15 AM


I would like to comment a bit further on the subject of the development pattern of an egg that has had the genes replaced by those of a different species. From your comments, I gather that the morphology of this egg development is not monitored by genes. Have I understood it correctly?

I have been intrigued by the organization of unicellular beings, like some algae, into colonies, that develop specialization, and therefore seem to be a precursor of pluricellular beings. Now, I compare both phenomena, and ask. Could this association and specialization have also nothing to do with genes? What is your opinion?

I will appreciate your comments


This message is a reply to:
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Wounded King
Member (Idle past 2199 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 7 of 70 (535201)
11-13-2009 5:39 PM
Reply to: Message 6 by straightree
11-13-2009 3:10 PM


I gather that the morphology of this egg development is not monitored by genes. Have I understood it correctly?

This depends on exactly what you mean. I think 'monitored' is the wrong term, the genes rather direct the development. Whose genes do this is the key fact here however. In cases like the Xenopus and Drosophila oocytes there are many proteins which are deposited in the egg by the mother, and these proteins affect the subsequent development of the embryo through its earliest stages. For this reason some oocytes, such as those of Xenopus can be mechanically stimulated to begin undergoing the first few cleavage stages even if the genetic material has been removed.

Could this association and specialization have also nothing to do with genes? What is your opinion?

I'd say almost certainly not. Although I'm not aware of any specific research into the genetic basis of coloniality/multicellularity in the Volvocales, which are perhaps the most commonly studied multicellular algal forms. I know that Chlamydomonas is often put forward as a model for the unicellular precursor of colonial algae.

TTFN,

WK


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Replies to this message:
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straightree
Member (Idle past 2855 days)
Posts: 57
From: Near Olot, Spain
Joined: 09-26-2008


Message 8 of 70 (535523)
11-16-2009 2:40 PM
Reply to: Message 7 by Wounded King
11-13-2009 5:39 PM


Whose genes do this is the key fact here however.

Maybe I miss some important point, but, if original genes are removed and replaced by those of another species, and development follows the pattern of original species, how can genes have directed this?


This message is a reply to:
 Message 7 by Wounded King, posted 11-13-2009 5:39 PM Wounded King has responded

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Dr Jack
Member (Idle past 209 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


(1)
Message 9 of 70 (535541)
11-16-2009 4:05 PM
Reply to: Message 8 by straightree
11-16-2009 2:40 PM


What do you think makes the proteins from the original egg mother?
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Wounded King
Member (Idle past 2199 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 10 of 70 (535547)
11-16-2009 4:46 PM
Reply to: Message 8 by straightree
11-16-2009 2:40 PM


Maybe I miss some important point, but, if original genes are removed and replaced by those of another species, and development follows the pattern of original species, how can genes have directed this?

There are a few possible outcomes in development of a SCNT embryo: In one the replacement DNA is from a species closely related enough that it produces a viable embryo, in which cases the eary embryonic stages are likely to be very similar anyway, for instance SCNT between llamas and camels can produce a viable embryo that will develop into a hybrid.

Another posibility is that, as Wells has been quoted saying in this thread, the genome are incompatible and the embryo dies at an early developmental stage, often after only one or two cell divisions. In certain animals, such as amphibians and insects, maternally deposited proteins and gene transcripts control the embryo for several stages of early development until what is called the mid-blastula transition (MBT), when the embryos own zygotic genes take over. Obviously in such embryos the compatibility of the genome is not relevant until the MBT.

So in some species the genes directing embryonic development until the MBT are those of the mother which deposited the proteins and mRNA in the oocyte.

TTFN,

WK

Edited by Wounded King, : No reason given.

Edited by Wounded King, : Sorry, I messed up the camel/llama example, it isn't actually SCNT at all, just cross species breeding, I should have gone back and checked the literature.


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Phydeaux
Junior Member (Idle past 3307 days)
Posts: 13
Joined: 11-17-2009


Message 11 of 70 (535611)
11-17-2009 1:07 AM
Reply to: Message 1 by Elhardt
10-19-2009 4:25 AM


I am just curious of when your video is coming out. Is your youtube name Elhardt?
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New Cat's Eye
Inactive Member


Message 12 of 70 (535672)
11-17-2009 10:22 AM
Reply to: Message 11 by Phydeaux
11-17-2009 1:07 AM


Is your evc name pronounced "Fido"?
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 Message 11 by Phydeaux, posted 11-17-2009 1:07 AM Phydeaux has responded

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Phydeaux
Junior Member (Idle past 3307 days)
Posts: 13
Joined: 11-17-2009


Message 13 of 70 (535673)
11-17-2009 10:24 AM
Reply to: Message 12 by New Cat's Eye
11-17-2009 10:22 AM


Yeah haha I actually had a discussion unregistered on polonium halos here before. Just thought I'd add more information lol than "yeah haha" lol

Edited by Phydeaux, : No reason given.


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deerbreh
Member (Idle past 997 days)
Posts: 882
Joined: 06-22-2005


(1)
Message 14 of 70 (535689)
11-17-2009 11:34 AM
Reply to: Message 5 by Wounded King
10-19-2009 9:15 AM


Mysterious Centrosomes?
Centrosomes are only mysterious to someone who is looking for a reason to claim Intelligent Design. And of course as you point out the notion that the centrosomes are inherited independently of DNA is nonsense. That is like saying the egg itself is independent of DNA. It isn't. DNA determined its structure, including the centrosomes and all of the other organelles.
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straightree
Member (Idle past 2855 days)
Posts: 57
From: Near Olot, Spain
Joined: 09-26-2008


Message 15 of 70 (535898)
11-18-2009 4:23 PM
Reply to: Message 10 by Wounded King
11-16-2009 4:46 PM


Thank you for your explanation. It is good to have an expert at hand!
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