Freethought & Rationalism Archive

Quetzal · 07-02-2002, 01:23 AM

Okay, I've run across a new one. I have a YEC, apparently a PhD microbiologist, who is arguing that macroevolution cannot occur because it would require the existence of novel protein families. He accepts things like frameshift mutation/amplification of the trypsinogen gene in Antarctic fish allowing production of glycoprotein, but argues that this is merely variation within a gene [i]family[i/]. When pressed, he has explained that protein folding peculiarities are what prevent this type of mutation from becoming a novel protein - and hence represent the barrier to created kinds.

Here's his folding argument in a nutshell:

Quote:

The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process shows what I claimed, that protein folds accompany cellular novelty - at least some of the time (if not most of the time). In other words if you pick almost any cellular cystem you will need new protein folds to constrcut them.

Your study of globin genes is a study within a gene family - they are all homologs or orthologs of a single gene. These could have arisen by either creation or evolution.

Protein folding is something that happens almost automatically to a protein chain of amino-acids ('chaperones' help but don't change the final structure). Only a very small subset of protein sequences will fold to a compact specific structure with a defined shape and surface that can do a job. It is an optimized process because it has been demonstrated that if the sequence isn't carefully chosen a protein would take millions of years to fold to it's native functional state.

If you constructed a random amino-acid sequence it will probably remain like a semi-extended string flopping around. A folded protein is quite rigid and most of the molecules in a population will have a near identical structure unlike a floppy chain.

The point that your textbooks are yet to make is that the proteins we study most of he time are coded for in genomes and are foldable (ie they automatically find the right shape to do their job). A good textbook will somewhere point out that most random amino-acid chains will not have this property.

And my point is that becasue protein structures are discontinuous in structure from one fold to another, and because protein folding is critically dependent on sequence, a protein typically will be unfolded (and hence non-functional) on the way to morphing into another protein fold via sequence changes. The point is that on the way to the new fold there is nothing good to select for so you are back to random sampling.(mispellings in the original) from <a href="http://www.evcforum.net/ubb/Forum5/HTML/000046-3.html#39" target="_blank">here</a>

He's now beyond my basic genetics knowledge. Anyone point me in the direction of good articles/websites that can refute this? Or anyone care to jab some large holes in his argument? Any help would be appreciated.

WinAce · 07-02-2002, 01:54 AM

I'm not a geneticist but I think this claim is based on some kind of error already.

Take, for example, human myoglobin and hemoglobin; they're structurally very similar but have quite different functions.

Producing a new gene from duplication and subsequent modification of an old one can create novel functions. Stacking several copies of old genes and modifying them can probably account for lots of those 'irreducibly complex' systems the ID'iots are always harping about.

This also should leave characteristic fingerprints, which we find in such complex genes (they look exactly like stacked-on copies of other genes with some differences added).

The common errors and stuff even in non-coding regions of such genes are quite compelling data for this hypothesis; such errors being produced by accident is quite unlikely.

I'm sure the knowledgeable people here will point you to some great resources to refute this newest junk.

Of course, ID arguments cut both ways--ask him what he thinks of such incredibly complex, glorious creatures that couldn't have possibly been produced by evolution such as the malaria parasite or tapeworm.

Quetzal · 07-02-2002, 02:45 AM

Alan: Thanks for your response. Unfortunately, this guy's come up with a new twist. The usual stuff isn't working. I've already bounced on both hemoglobin (note paragraph 2 of his response) and cooption and amplification (the trysinogen example). He just hand waves it away with the usual "that's just microevolution within a gene family" that we always hear in "kinds" arguments.

His argument appears to rest on two premeses:

1. Macroevolution - change in higher taxa - requires the creation of novel protein families - not the cooption of existing genes to new functions. I would be willing to bet that this is in error, but don't have the background to nail him down.

2. Novel protein families cannot gradually evolve from other proteins because of the way proteins are structured (folding). Again, I sense this is fundamentally flawed, but I don't have the background to tackle it.

There also appears to be something about randomness and specificity buried in there somewhere, but I can't winkle it out.

It's kind of a unique experience: an intelligent creationist with a new argument.

07-02-2002, 03:07 AM

Even if there were no flaws in his argument about proteins (I don't know enough to attack this), it would merely represent a problem within evolutionary theory. It sure as hell wouldn't prove creationism was right. So I still feel that "intelligent creationist" is a bit of an oxymoron.

Oolon Colluphid · 07-02-2002, 03:12 AM

Hi Morpho.

1. It�s up to him to demonstrate that this irreducible complexity really is irreducible, not up to you to find a way of reducing it. In science, there�s no harm in saying we don�t know. All that leaves is a question mark. But the burden is on him to demonstrate that one protein really couldn�t have morphed into another, and so must have been created. So far he seems to be just saying so.

2. Could the protein-coding DNA not have been doubled, and one of the copies pass through a non-functional stage before further mutation reactivated it? Fine, have an unfolded-protein code... that�s not used. Sure it�s a just-so story, but all such hypothesising will be any way.

3. my old stand-by: say �okay, fine, it�s irreducible�, and ask him how his alternative explains the fossil record, the laryngeal nerve and the coccyx!

Cheers, Oolon

Oolon Colluphid · 07-02-2002, 03:19 AM

Oh, and you could get him to define �kind�, and see how these protein families match up with that. I�ll bet the two don�t match. If a created kind roughly = Family, say, are there discontinuities in the protein families between them? Do the relevant proteins vary from genus to genus, with only unfolded intermediates? If not, if it�s any higher taxon, then humans and apes are one �kind� anyway (the key point that creationists will never admit).

Oolon

pz · 07-02-2002, 04:53 AM

Quote:

Originally posted by Morpho:

His argument appears to rest on two premeses:

1. Macroevolution - change in higher taxa - requires the creation of novel protein families - not the cooption of existing genes to new functions. I would be willing to bet that this is in error, but don't have the background to nail him down.

This really doesn't make much sense. The existence of gene families that are found across many different phyla is one of the evidences for evolution. Ask him to be specific: what gene families distinguish chordate from arthropod taxa, for instance?

Quote:

2. Novel protein families cannot gradually evolve from other proteins because of the way proteins are structured (folding). Again, I sense this is fundamentally flawed, but I don't have the background to tackle it.

This is wrong in multiple ways. First, there is no requirement that proteins need to change gradually: one of my favorite genes, the homeobox gene Goosecoid that plays an important role in axis specification in vertebrate development, is clearly the result of a fusion between two genes, bicoid and gooseberry, that can be found in invertebrates. Secondly, he's being vague and doing nothing but blindly naysaying something. Pin him down. Get him to name a gene family that he thinks is inviolable. What you'll find is that there is a large amount of diversity within the family (which is why it is called a gene family in the first place! I'm at a loss to see how he can call gene families evidence for an inability of a protein to change when when differences between related proteins are their hallmark) indicative of evolutionary change, You'll also find that either a) the gene family is present in many or all taxa, so its failure to change cannot be a barrier to macroevolution, or b) you will be able to find papers in the literature that describe its affinities to other gene families, showing a pattern of change.

The last thing you want to do is let him dictate the discussion by confining it to handwaving about generalities, where it can only be resolved on the basis of how authoritative someone sounds. Creationists are masters at putting up a pretense of certainty.

pseudobug · 07-02-2002, 05:52 AM

Some nice replies in this thread.

FWIW, I think this creationist yo-yo is full of feces. If he thinks the development of novel protein families are a barrier to macroevolution, ask the idiot why a boatload of bacteria-->mammals use the TCA cycle and glycolytic pathways in energy metabolism/generatioin of reducing equivalents. Furthermore, ask him about the structural and functional similarities between proteins involved in photosynthesis and the visual systems in higher mammals.

Basically, this fundie/creationist you are engaged with is as full of crap as a Christmas goose.

theyeti · 07-02-2002, 07:11 AM

Morpho, the evolution of new folds from existing folds has been demonstrated with at least a few proteins.* While folds are often separated in sequence space by regions of high energy (i.e. bad folds), these regions can be "tunneled" through by recombination. Futhermore, there are a limited number of folds that are seen in nature (around a few hundred up to maybe a thousand, but it depends on how you classify them), despite a near infinite number of possibilities. Consider that a complex organism like a human has around 100,000 proteins, each of which may have several folds, and you can see that the number of folds is actually quite small. This indicates that most proteins are descended from a relatively small number of progentiors. So therefore 99% of evolution can be explained by changes within fold families. Moreover, you can generate an almost infinite amount of variability simply by suffling various folds in multi-domain proteins (through exon suffling, fusion, etc.). Other points have already been covered, esp. in regards to the irrelevancy for macroevolution. (I would be very surprised if there are any unique folds in humans as compared to chimps).

At best, your YEC's objection only holds for the origin of life, where presumably there would have had to have been some significant number of already present folds to get a viable organism, but even that's questionable, since partially folded or even unfolded proteins can be functional (it's just that in modern cells, these things tend to be chopped up by proteases or form aggregates due to crowding). And given the abundance of different scenarios (e.g RNA world) the need for folded proteins may not exist depending on the model you're working with.

* For best example, see:

<a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=118012 40&dopt=Abstract" target="_blank">FEBS Lett 2002 Jan 16;510(3):133-5</a>, A common evolutionary origin of two elementary enzyme folds.

Quote:

The (beta alpha)(8)-barrel is the most frequent and most versatile fold among enzymes [Hocker et al., Curr. Opin. Biotechnol. 12 (2001) 376-381; Wierenga, FEBS Lett. 492 (2001) 193-198]. Structural and functional evidence suggests that (beta alpha)(8)-barrels evolved from an ancestral half-barrel, which consisted of four (beta alpha) units stabilized by dimerization [Lang et al., Science 289 (2000) 1546-550; Hocker et al., Nat. Struct. Biol. 8 (2001) 32-36; Gerlt and Babbitt, Nat. Struct. Biol. 8 (2001) 5-7]. Here, by performing a comprehensive database search, we detect a striking and unexpected structural and amino acid sequence similarity between (beta alpha)(4) half-barrels and members of the (beta alpha)(5) flavodoxin-like fold. These findings provoke the hypothesis that a large fraction of the modern-day enzymes evolved from a basic structural building block, which can be identified by a combination of sequence and structural analyses.

I would suggest getting those other articles mentioned in the abstract, and also check out the <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=PubMed&cmd=Display&dopt=pubmed_pubme d&from_uid=11801240" target="_blank">related articles</a>.

Also, new folds have been generated via in vitro evolution and by screening random libraries. See <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=115899 99&dopt=Abstract" target="_blank">Trends Biochem Sci 2001 Oct;26(10):577-9</a>, Protein-fold evolution in the test tube. and related articles.

Another article of interest is <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=115511 77&dopt=Abstract" target="_blank">J Struct Biol 2001 May-Jun;134(2-3):167-85</a>, Fold change in evolution of protein structures.

Quote:

Typically, protein spatial structures are more conserved in evolution than amino acid sequences. However, the recent explosion of sequence and structure information accompanied by the development of powerful computational methods led to the accumulation of examples of homologous proteins with globally distinct structures. Significant sequence conservation, local structural resemblance, and functional similarity strongly indicate evolutionary relationships between these proteins despite pronounced structural differences at the fold level. Several mechanisms such as insertions/deletions/substitutions, circular permutations, and rearrangements in beta-sheet topologies account for the majority of detected structural irregularities. The existence of evolutionarily related proteins that possess different folds brings new challenges to the homology modeling techniques and the structure classification strategies and offers new opportunities for protein design in experimental studies.

{my emphasis}

If I come across any other good articles, I'll post them for you.

theyeti

[ July 02, 2002: Message edited by: theyeti ]

theyeti · 07-02-2002, 08:21 AM

Wow, here's one that I hadn't seen before:

<a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=115274 43&dopt=Abstract" target="_blank">J Theor Biol 2001 Sep 7;212(1):35-46</a>, Exploring protein sequence space using knowledge-based potentials.

Quote:

Knowledge-based potentials can be used to decide whether an amino acid sequence is likely to fold into a prescribed native protein structure. We use this idea to survey the sequence-structure relations in protein space. In particular, we test the following two propositions which were found to be important for efficient evolution: the sequences folding into a particular native fold form extensive neutral networks that percolate through sequence space. The neutral networks of any two native folds approach each other to within a few point mutations. Computer simulations using two very different potential functions, M. Sippl's PROSA pair potential and a neural network based potential, are used to verify these claims

{my empahsis}

The authors go on to verify this with their computer modeling. This is from the conclusions:

Quote:

Neutral paths within the sets S(t) extend to
almost the length of the amino acid sequence.
The neutral sets therefore form extensive neutral networks that percolate the entire sequence space. The existence of extensive neutral networks meets a claim raised by Maynard-Smith (1970) for protein spaces that are suitable for efficient evolution. Very different types of computational models agree on the existence of structurally neutral networks, in particular knowledge-based potentials off-lattice (Babajide et al., 1997), and lattice model with simplified alphabets (Bornberg-Bauer, 1997; Govindarajan & Goldstein, 1997; Bastolla et al., 1999). Empirical evidence for a large degree of functional neutrality in protein space is indeed observed (Martinez et al.,1996).
[...]
Our computational data support an even stronger claim: sequences that fold into two completely different native structures need not differ by more than a few crucial amino acids.

{emphases original}

Given that these are computational studies, you've got to take them with a grain of salt, but they do seem to follow what's been found empirically. If what the authors say is true, then there is no barrier to evolving new folds from existing folds via point mutation alone. Add to that things like recombination, and the "new folds can't evolve" objection is obliterated.

theyeti

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07-02-2002, 01:54 AM	#2
WinAce Beloved Deceased Join Date: Feb 2002 Location: Carrboro, NC Posts: 1,539	I'm not a geneticist but I think this claim is based on some kind of error already. Take, for example, human myoglobin and hemoglobin; they're structurally very similar but have quite different functions. Producing a new gene from duplication and subsequent modification of an old one can create novel functions. Stacking several copies of old genes and modifying them can probably account for lots of those 'irreducibly complex' systems the ID'iots are always harping about. This also should leave characteristic fingerprints, which we find in such complex genes (they look exactly like stacked-on copies of other genes with some differences added). The common errors and stuff even in non-coding regions of such genes are quite compelling data for this hypothesis; such errors being produced by accident is quite unlikely. I'm sure the knowledgeable people here will point you to some great resources to refute this newest junk. Of course, ID arguments cut both ways--ask him what he thinks of such incredibly complex, glorious creatures that couldn't have possibly been produced by evolution such as the malaria parasite or tapeworm.

07-02-2002, 02:45 AM	#3
Quetzal Senior Member Join Date: Nov 2001 Location: Ecuador Posts: 738	Alan: Thanks for your response. Unfortunately, this guy's come up with a new twist. The usual stuff isn't working. I've already bounced on both hemoglobin (note paragraph 2 of his response) and cooption and amplification (the trysinogen example). He just hand waves it away with the usual "that's just microevolution within a gene family" that we always hear in "kinds" arguments. His argument appears to rest on two premeses: 1. Macroevolution - change in higher taxa - requires the creation of novel protein families - not the cooption of existing genes to new functions. I would be willing to bet that this is in error, but don't have the background to nail him down. 2. Novel protein families cannot gradually evolve from other proteins because of the way proteins are structured (folding). Again, I sense this is fundamentally flawed, but I don't have the background to tackle it. There also appears to be something about randomness and specificity buried in there somewhere, but I can't winkle it out. It's kind of a unique experience: an intelligent creationist with a new argument.

07-02-2002, 03:07 AM	#4
DMB Guest Posts: n/a	Even if there were no flaws in his argument about proteins (I don't know enough to attack this), it would merely represent a problem within evolutionary theory. It sure as hell wouldn't prove creationism was right. So I still feel that "intelligent creationist" is a bit of an oxymoron.

07-02-2002, 03:12 AM	#5
Oolon Colluphid Contributor Join Date: Sep 2000 Location: Alibi: ego ipse hinc extermino Posts: 12,591	Hi Morpho. 1. It�s up to him to demonstrate that this irreducible complexity really is irreducible, not up to you to find a way of reducing it. In science, there�s no harm in saying we don�t know. All that leaves is a question mark. But the burden is on him to demonstrate that one protein really couldn�t have morphed into another, and so must have been created. So far he seems to be just saying so. 2. Could the protein-coding DNA not have been doubled, and one of the copies pass through a non-functional stage before further mutation reactivated it? Fine, have an unfolded-protein code... that�s not used. Sure it�s a just-so story, but all such hypothesising will be any way. 3. my old stand-by: say �okay, fine, it�s irreducible�, and ask him how his alternative explains the fossil record, the laryngeal nerve and the coccyx! Cheers, Oolon

07-02-2002, 03:19 AM	#6
Oolon Colluphid Contributor Join Date: Sep 2000 Location: Alibi: ego ipse hinc extermino Posts: 12,591	Oh, and you could get him to define �kind�, and see how these protein families match up with that. I�ll bet the two don�t match. If a created kind roughly = Family, say, are there discontinuities in the protein families between them? Do the relevant proteins vary from genus to genus, with only unfolded intermediates? If not, if it�s any higher taxon, then humans and apes are one �kind� anyway (the key point that creationists will never admit). Oolon

07-02-2002, 05:52 AM	#8
pseudobug Regular Member Join Date: Jan 2002 Location: land of confusion Posts: 178	Some nice replies in this thread. FWIW, I think this creationist yo-yo is full of feces. If he thinks the development of novel protein families are a barrier to macroevolution, ask the idiot why a boatload of bacteria-->mammals use the TCA cycle and glycolytic pathways in energy metabolism/generatioin of reducing equivalents. Furthermore, ask him about the structural and functional similarities between proteins involved in photosynthesis and the visual systems in higher mammals. Basically, this fundie/creationist you are engaged with is as full of crap as a Christmas goose.

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