Uncommon Descent Serving The Intelligent Design Community

Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

Jonathan Wells Jonathan Wells, the author of The Myth of Junk DNA, offers some thoughts on the limitations of what DNA does. Read this before you pay attention to any more DNA fundamentalism:

We have rigorous experimental evidence that DNA does not even code completely for proteins; in most cases the final forms of proteins are not fully specified by DNA sequences.

After transcription, most multi-exon eukaryotic genes undergo alternative splicing, which changes the sequence. [1] We know of one DNA sequence (a “gene” in now-obsolete parlance) in Drosophila from which over 18,000 different proteins are derived, mostly through alternative splicing. [2]

After alternative splicing, some mRNAs undergo editing, in which various subunits are modified or removed and new subunits are added. [3] Because of alternative splicing and RNA editing, the sequences of most mRNAs are different from the original DNA sequence. Instead, their final forms are specified by processes mediated by huge epigenetic complexes (spliceosomes and editosomes) that respond to extracellular cues and operate differently in different developmental stages.

Even after RNAs are translated into proteins, the latter change in ways that cannot be traced back to DNA sequences. First, proteins with the same amino acid sequences can adopt different three-dimensional folding patterns; these are called “metamorphic proteins.” [4] Second, most proteins are glycosylated: That is, complex carbohydrates are chemically bonded to them to generate enormous diversity in protein functions. [5] Since carbohydrate molecules are branched, they carry many more orders of magnitude of information than linear molecules such as DNA and RNA. This has been called the “sugar code,” and although it is highly specified it is largely
independent of DNA sequence information. [6]

So DNA does not completely specify proteins; but even if it did, it would not specify their spatial locations in the cell or embryo. After a protein is transcribed in the nucleus, it must be transported to the proper location in the cell with the help of cytoskeletal arrays and membrane-bound targets that are not themselves specified solely by DNA sequences. The pattern of spatial information in the membrane — called the “membranome” — is known not to be specified by DNA [7] Since spatial localization is essential for proteins to function properly, this adds yet another layer of complexity to the specification of form and function. [8]

Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.

[1] Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, et al. (2013) Alternative splicing: A pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol 14:153-165. doi:10.1038/nrm3525

[2] Sun W, You X, Gogol-Döring A, He H, Kise Y, et al. (2013) Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing. EMBO J Jun 21, 2013. doi:10.1038/emboj.2013.144

[3] Peng Z, Cheng Y, Tan BC, Kang L, Tian Z, et al. (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253-260. doi:10.1038/nbt.2122

[4] Bryan PN, Orban J (2010) Proteins that switch folds. Curr Opin Struct Biol 20:482-488. doi:10.1016/j.sbi.2010.06.002

[5] Furukawa K, Ohkawa Y, Yamauchi Y, Hamamura K, Ohmi Y, et al. (2012) Fine tuning of cell signals by glycosylation. J Biochem 151:573-578. doi:10.1093/jb/mvs043

[6] Gabius H-J (2000) Biological information transfer beyond the genetic code: The sugar code. Naturwissenschaften 87:108-121. doi:10.1007/s001140050687

[7] Cavalier-Smith T (2004) The membranome and membrane heredity in development and evolution. In: Hirt RP, Horner DS, eds. Organelles, Genomes and Eukaryote Phylogeny. CRC Press (Boca Raton, FL) pp 335-351.

[8] Wells J (2013) The membrane code: A carrier of essential biological information that is not specified by DNA and is inherited apart from it. In: Marks RJ II, Behe MJ, Dembski WA, Gordon BL, Sanford JC, eds. Biological Information: New Perspectives. World Scientific (Singapore) pp 474-488.

Follow UD News at Twitter!

Comments
Quick blurb at Stanford on above paper in comment #211... Face facts: Researchers discover long-ignored DNA segments that coordinate early face development DATCG
April 4, 2014
April
04
Apr
4
04
2014
05:48 AM
5
05
48
AM
PST
So-Called "Junk" DNA influence on facial form developmental process... Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
"Beyond providing a direct link between the signaling environment and the transcriptional machinery controlling NC function, the importance of identifying such ligand in the future is underscored by observations that human craniofacial development is particularly sensitive to environmental changes resulting from fetal exposure (Lammer et al., 1985)."
Wiki... Neural Crest - cells are a transient, multipotent, migratory cell population unique to vertebrates that gives rise to a diverse cell lineage including melanocytes, craniofacial cartilage and bone, smooth muscle, peripheral and enteric neurons and glia.[1] Just the beginning of discovery in Epigenetics and the Epigenome.DATCG
April 4, 2014
April
04
Apr
4
04
2014
05:38 AM
5
05
38
AM
PST
Epigenetics: The sins of the father In relation to new discoveries and Epigenetics... "'It's a huge black box,' Lane says" Controversial...
The subject remains controversial, in part because it harks back to the discredited theories of Jean-Baptiste Lamarck, a nineteenth-century French biologist who proposed that organisms pass down acquired traits to future generations. To many modern biologists, that's “scary-sounding”, says Oliver Rando, a molecular biologist at the University of Massachusetts Medical School in Worcester, whose work suggests that such inheritance does indeed happen in animals3. If it is true, he says, “Why hasn't this been obvious to all the brilliant researchers in the past hundred years of genetics?”.
DATCG
April 4, 2014
April
04
Apr
4
04
2014
05:13 AM
5
05
13
AM
PST
Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes "This indicates that the complexity of the mammalian genome, especially the transcriptome, cannot be interpreted merely according to the central dogma of molecular biology “DNA-RNA-protein."DATCG
April 4, 2014
April
04
Apr
4
04
2014
04:57 AM
4
04
57
AM
PST
AVS, you completely wrong. Wells is talking about alternative splicing, which edits mRNA with respect to exons. Alternative splicing is influenced by epigenetic factors. Hence, the DNA doesn't specify the ultimate protein. Of course exons included in the final protein will have the anticipated amino acid sequence but other exons may not be expressed at all. Which exons will be expressed cannot be predicted from the DNA alone because ... wait for it ... alternative splicing is influenced by epigenetic factors.Jehu
April 3, 2014
April
04
Apr
3
03
2014
04:28 PM
4
04
28
PM
PST
Joe, you might appreciate this: New level of genetic diversity in human RNA sequences uncovered - May 2011 Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person's genetic material." http://www.physorg.com/news/2011-05-genetic-diversity-human-rna-sequences.htmlbornagain77
April 3, 2014
April
04
Apr
3
03
2014
12:38 PM
12
12
38
PM
PST
AVS, you are a liar and a moron. Wells statement is not ambiguous. But thanks for showing us all you can do is accuse others of your faults. And the only pseudoscience bullshit is coming from your hole.Joe
April 3, 2014
April
04
Apr
3
03
2014
09:02 AM
9
09
02
AM
PST
It's already been demonstrated that his statement was ambiguous. By you no less, Joe. Thank you for making yourself look like a complete imbecile. Take care now and have fun peddling this pseudoscience bullshit of yours.AVS
April 3, 2014
April
04
Apr
3
03
2014
08:46 AM
8
08
46
AM
PST
AVS:
My issue is with the statement “protein is not fully specified by DNA.”
It isn't
amino acid sequence is completely specified by the DNA
'The amino acid sequence doesn't make the protein. And no, Wells did NOT make any ambiguous statements. AVS is just too stupid to be able to comprehend what Wells said. AVS is a moron and a liar.Joe
April 3, 2014
April
04
Apr
3
03
2014
04:28 AM
4
04
28
AM
PST
No. It doesn't matter which exons are expressed as far as this conversation is concerned, what matters is the sequence of the DNA and the amino acid sequence that comes from it. They will always match. Not only is Wells wrong but even more unforgivable is how vague his claim are. He words things poorly and in a way that seems to support his position. Wells' audience is largely scientifically illiterate and lacking any knowledge in biology so I would expect him to spell every detail out. Instead he makes ambiguous claims (as Joe has already demonstrated) in order to paint a picture of "scientific support."AVS
April 3, 2014
April
04
Apr
3
03
2014
12:25 AM
12
12
25
AM
PST
The issue is not whether the amino acid sequence matches the corresponding exon but which exons are expressed in the ultimate protein.Jehu
April 3, 2014
April
04
Apr
3
03
2014
12:11 AM
12
12
11
AM
PST
My issue is with the statement "protein is not fully specified by DNA." The amino acid sequence is completely specified by the DNA, you can take the amino acid sequence, and 99% of the time it will exactly match the predicted sequence from the corresponding DNA exon. RNA editing accounts for the 1% that doesn't. The majority of alternative splicing also functions through the recognition of the nucleotide sequence by spliceosome proteins and bound RNA. This means that the majority of splicing also functions by sequence specificity; sequences directly taken from DNA.AVS
April 2, 2014
April
04
Apr
2
02
2014
05:28 PM
5
05
28
PM
PST
Anyway AVS, alternative splicing is influenced by epigenetic factors and changes the ultimate protein, hence the protein is not fully specified by the DNA. Alternative splicing is not rare and occurs in over 90% of human genes. In at least one case, alternative splicing can result in over 38,000 different proteins from a single gene.Jehu
April 2, 2014
April
04
Apr
2
02
2014
05:14 PM
5
05
14
PM
PST
kairosfocus @ 194
D: The alleged can readily be set aside in both cases, especially that of the good Canon. KF
Yes, that's a good point. I accept the correction. Thank you.Dionisio
April 2, 2014
April
04
Apr
2
02
2014
04:47 PM
4
04
47
PM
PST
RodW, How can we test the claim that organisms are the sum of their genome? Rodent's bizarre traits deepen mystery of genetics, evolution:
The study focuses on 60 species within the vole genus Microtus, which has evolved in the last 500,000 to 2 million years. This means voles are evolving 60-100 times faster than the average vertebrate in terms of creating different species. Within the genus (the level of taxonomic classification above species), the number of chromosomes in voles ranges from 17-64. DeWoody said that this is an unusual finding, since species within a single genus often have the same chromosome number. Among the vole's other bizarre genetic traits: •In one species, the X chromosome, one of the two sex-determining chromosomes (the other being the Y), contains about 20 percent of the entire genome. Sex chromosomes normally contain much less genetic information. •In another species, females possess large portions of the Y (male) chromosome. •In yet another species, males and females have different chromosome numbers, which is uncommon in animals. A final "counterintuitive oddity" is that despite genetic variation, all voles look alike, said DeWoody's former graduate student and study co-author Deb Triant. "All voles look very similar, and many species are completely indistinguishable," DeWoody said. In one particular instance, DeWoody was unable to differentiate between two species even after close examination and analysis of their cranial structure; only genetic tests could reveal the difference. Nevertheless, voles are perfectly adept at recognizing those of their own species.
Yup after all this “evolution” a vole is still a vole.Joe
April 2, 2014
April
04
Apr
2
02
2014
04:40 PM
4
04
40
PM
PST
AVS- Shut up. You have proven to be a moron and a poseur. You are also a liar and misrepresent Wells. I have forgotten more about science than you will ever know- and I don't forget. You are a pathetic excuse for a human.Joe
April 2, 2014
April
04
Apr
2
02
2014
04:35 PM
4
04
35
PM
PST
"Darwin was wrong and lamarck was right" Wow that's a pretty bold statement there Andre. In fact it's another statement that completely proves you have no idea what you are talking about. While I am fine with arguing that epigenetics may support lamarckian evolution, it only represents a small portion of what is going on. The majority of evolution occurs at the level of DNA initially, as "darwinism" suggests. Andre, read my post to Joe, you're in the same boat as him. You may actually be slightly more intelligent than him, but that's not saying much.AVS
April 2, 2014
April
04
Apr
2
02
2014
04:09 PM
4
04
09
PM
PST
I never said alternative splicing was rare, Jehu. Joe, talking to you is exactly like trying to explain a biological principle to someone with absolutely no science background. This is exactly what happened to me today, and I thought in my head as the conversation went on "this is exactly how the conversations at UD go." No matter what comes out of my mouth, you are going to remain in a state of confusion. You are completely clueless when it comes to science, especially biology. For this reason, I will not even attempt to try to talk about biology any further with you.AVS
April 2, 2014
April
04
Apr
2
02
2014
04:04 PM
4
04
04
PM
PST
D: The alleged can readily be set aside in both cases, especially that of the good Canon. KFkairosfocus
April 2, 2014
April
04
Apr
2
02
2014
03:37 PM
3
03
37
PM
PST
Polish astronomer Kopernik (allegedly a believer in God) and Italian astronomer Galileo (also allegedly a believer in God) were convinced by the strong evidences they observed, so they went against the widely and firmly established Aristotelian thinking of their times. The rest is known history. Can history repeat itself?Dionisio
April 2, 2014
April
04
Apr
2
02
2014
02:33 PM
2
02
33
PM
PST
Joe said,
In any case, if the major source of information on form is not genetic information where does it come from? Other parts of the cell including its cytoskeleton and membrane.
I'd say this is correct, the cytoskeleton and membrane do store information in a sense and pass that down to subsequent generations. There are many other such sources of information...one could even say the cell itself is a source. DNA doesnt specify how to make a cell or organism from scratch, it only specifies how maintain a cell or grow an organism within the context of a living cell or zygote. But I think Wells dismisses the role of DNA too easily. The cytoskeleton may store information but the actin and tubulin proteins that make up the cytoskeleton are coded for in the DNA. The proteins that interact with them and allow the cytoskeleton to store info are also coded in the DNA of course..and all of these are turned on and off by regulatory elements coded in the DNA. Heres another example of what your talking about: An alligator egg is developing. Where is the information that will determine whether its a male or female? Its not in the DNA, its the outside air temperature that will determine it. The only way you could predict boy alligator versus girl would be to know the air temp! Of course, its molecular machinery within the developing embryo, coded for by the DNA, that responds to the air temperature and directs the developing embryo to a particular fateRodW
April 2, 2014
April
04
Apr
2
02
2014
02:10 PM
2
02
10
PM
PST
BTW, AVS, alternative splicing is not rare, it occurs in well over 90% of human genes.Jehu
April 2, 2014
April
04
Apr
2
02
2014
01:50 PM
1
01
50
PM
PST
Which brings us full circle AVS..... Darwin was wrong and Lamarck was right.....Andre
April 2, 2014
April
04
Apr
2
02
2014
01:42 PM
1
01
42
PM
PST
AVS
Wells’ argument is that alternative splicing results in a difference in the amino acid sequence and [sic] what would be expected from the DNA coding regions.
No, Wells' argument is that the final forms of proteins are often not fully specified by the DNA. Which is true because alternative splicing is influenced by epigenetic inputs.Jehu
April 2, 2014
April
04
Apr
2
02
2014
01:36 PM
1
01
36
PM
PST
AVS- you are a liar and a moron. How did I contradict myself?Joe
April 2, 2014
April
04
Apr
2
02
2014
01:23 PM
1
01
23
PM
PST
AVS It sights proper references and highlights the differences between Darwinian evolution and Lamarckian evolution, its important to know that they are two opposing views. Epigenetics are NOT part of your Darwin based view, to say that it is makes you liar....Andre
April 2, 2014
April
04
Apr
2
02
2014
01:22 PM
1
01
22
PM
PST
Other parts of the cell including its cytoskeleton and membrane. AVS:
Care to explain this in your own words Joe?
Are you admitting ignorance of developmental biology? Sweet. Well, for one, the cytoskeleton contains micro-tubules that allow proteins to get where they are needed where they are needed.Joe
April 2, 2014
April
04
Apr
2
02
2014
01:21 PM
1
01
21
PM
PST
Joe, this is what you said yesterday: "He is talking about the DNA sequence is different from the processed mRNA sequence" You just completely contradicted yourself, congrats. You are a blubbering troll with no knowledge in the field of biology. Have a nice life.AVS
April 2, 2014
April
04
Apr
2
02
2014
01:18 PM
1
01
18
PM
PST
AVS spews:
Yes, we know Joe, you think he’s referring to the mRNA sequence.
Nope, I don't think tat. Just read what he says, moron. And I don't care what Sal says. That doesn't change the fact that Wells was referring to TRANSCRIPTION which does NOT involve amino acid sequences. So stop being a dishonest ass for once in your life.Joe
April 2, 2014
April
04
Apr
2
02
2014
01:13 PM
1
01
13
PM
PST
"Other parts of the cell including its cytoskeleton and membrane." Care to explain this in your own words Joe?AVS
April 2, 2014
April
04
Apr
2
02
2014
01:10 PM
1
01
10
PM
PST
1 2 3 8

Leave a Reply