IAP Political Forum

For years evolutionists have been making hay over the claim that Chimps and Humans are genetically similar to about 99%.  Well it seems that much of that was hype.  The similarities are less than thought and now it appears they are converging on a figure near 94%.  Well below the similarity for mice at nearly 98%.  This is significant because at the same time we have learned how evolution has not been able to produce even one new protein interaction in the billions and billions and billions of lab organisms observed and yet these genetic differences between humans and chimps include thousands of them. 

How can it be?  Evolutionists estimate that the population pool involved in the presumed evolution of humans from ancestral apes is less than 20 billion and in that pool thousands of significant protein structure differences must have occurred if evolution is correct.  Well if so, this completely contradicts experimental biology and molecular biology studies which show that known evolutionary processes don't generate these kinds of changes given the low population density and probability analysis provides the theoretical basis to demonstrate why this is the case.  In order to generate these changes given observed processes, the population pool must be increased billions and billions and billions and billions of time over.

The conclusion should be obvious.  Some process other than random mutation, and the other evolutionary processes along with natural selection had to be involved.

The article below describes how genetics researchers are backing away from the 1% difference claim but it does not discuss the implications directly.  I have added that here for additional possible discussion.

Truth be Told about Human Chimp DNA (http://www.arn.org/blogs/index.php/literature/2007/07/02/truth_be_told_about_chimp_human_dna_comp)

Comparing genomes is difficult when there are large rearrangements or several small, such as a difference in gene copy number. The main difference between chimp and humans is that human have two chimp chromosomes spliced into one. The divergence rate is 1.23% when comparing orthologous (http://en.wikipedia.org/wiki/Ortholog#Orthology) sequences (source (http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html)), coding regions produce almost identical proteins (from the same source)


In the meantime, there has been more chromosomal rearrangements between mouse and human (as obvious already from the difference in chromosome number, chimp - 48, human -46, mouse - 40, there are a lot more of other inter and intra chromosomal rearrangements between mouse and human than between chimp and human, google "syntheny maps"). You can't directly compare sequences if portions of it were translocated or inverted. Or to be precise, you can, but you must use the same model for comparison. From your links, the choice of method is unclear, 30 years ago melting temperature of DNA heteroduplexes was used, you really can't compare that to methods based on nucleotide sequences.

As for comparing all three genomes, pick individual orthologous gene sequence or noncoding regions and compare them. Below is just an example, but if you increase the number of compared othologs, the human-mouse divergence rate will always be obviously larger than human-chimp.

Example, hemoglobin, alpha 1, first 60 nucleotides of coding region (from genebank, acession numbers NM_000558, NM_001042626, NM_008218)

human: atggtgctgt ctcctgccga caagaccaac gtcaaggccg cctggggtaa ggtcggcgcg
chimp:  atggtgctgt ctcctgccga caagaccaac gtcaaggccg cctggggtaa ggtcggcgcg
mouse: atggtgctct ctggggaaga caaaagcaac atcaaggctg cctgggggaa gattggtggc

pick a gene, any gene

Similarities are interesting but they only tell part of the story.  It is the differences that reveal inherent weaknesses in the  evolutionary narrative.  How do you address them?

It is difficult for me to explain details because I don't know your background. I will just focus on 2 things at the moment.


1. It does takes a lot of time for a large population to accumulate changes, but it is assumed that trough most time the population of human species or closely related species did not went over 100 000. Effective population size is usually 10% of that and bottleneck effect are common in evolutionary history. In such small populations mutations can fixate much faster. In addition, mutations are not generated every generation, but during every DNA replication. Gametes in male sperm undergo thousands and thousands of replications in individual's reproductive period.

2. Measuring difference between 2 organisms. OK, lets simplify this and instead of nucleotide strings take "reasoned faith"

- comparing "reasoned faith" and "reasoned faith" - 100% similarity = identical
- comparing "reasoned faith" and "reasones faith" - 1 difference =12/13 92% identity
- comparing "reasoned faith" and "faith reasoned" - hm... aligning these two strings as a whole would give 0 identity = 0%.

But in fact it is a result of a single mutation event, just like in "reasones faith". So should it be equivalent to the 92% ? Using some methods, it would be 100% identical, because only individual othologs would be directly compared "reasoned" with "reasoned" and "faith" with "faith". To include single changes and indels and translocations in a pack, a scoring system is usually used, but preferably all three are described separately.

Well first off it isn't "The Truth Is Now Told About Chimp DNA"; this implies there was a lie, and there wasnt. They were simply incorrect, off by a bit. Could be they're still wrong. Could be we find out in 10 years it's 99% like ours, or more alike with 'more important' dna. This happens when you're actually looking for an answer rather than simply sitting back re-assured in any answer you come up with and prove with mere faith is the right one.


I don't see why that conclusion is obvious in the least. In fact I don't even see what it has to do with it. There is only one thing to conclude when faced with an unknown: that it is unknown. Blackness. A big question mark. Nothing 'obvious' about it. It's not a cue to insert any answer.



Ahk

Fair enough Ahk, we embellished for dramatic effect.


I suppose, one way that the results are confused is by how you score differences.   Some are scored by base pair differences while other disregard amino acid substitutions that are thought to be inconsequential.   I agree that the key is in the "important" differences.  These are the protein binding site and gene control sequences for example and it is these differences that I am attempting to discuss.  Since evolutionary processes are unable to account for these alterations, I wonder how the narrative will be adjusted as this reality becomes better realized.


It is interesting that you say this because this is not the way the scientific method is described.   The process is to form a hypothesis and then test it with observation and experiment.  If the observations and experiments don't match the hypothesis  then you conclude the hypothesis is incorrect and you move on to a new one.

In the case of evolution, experiments and observation over the past 50 years demonstrate clearly that known evolutionary processes don't form new protein-protein interactions.  Meanwhile probability analysis provides the explanation.   Studies of 3D shape space together with electro-chemical affinities show us that most interactions require six consecutive specific amino acid combinations to generate a new binding site.  For most proteins given the number of base pairs and the mutation rate, this would require a pool of 10^40 or more organisms just to create one new interaction by known processes.  Meanwhile biologists estimate there have only been 10^35 or so organisms in existence on earth in the entire time span.

So how do we resolve this?  Do we really leave this as an unknown or do we begin to look for a better hypothesis? 

Also where is the proper assignment of the unknown?  Is it that macro-evolution is correct, we just don't know how it happened and cannot demonstrate right now that it did happen?  Or is it that common descent is correct we just don't know what processes were involved?  Or is it that we don't know what is correct and what isn't correct?

Thomas Hunt Morgan (Nobel prize in 1933). Almost all known mutant fruit flies with drastic phenotype changes (result of changed protein-protein interaction) were produced in the lab.

What this always comes down to is that since science cannot explain everything it must be flawed. Of course it's 'flawed'. We can't even explain a circle. Not the point. An unknown is an unknown.


You put the cart before the horse. If there is an unknown all that can be done is further examination. The process you describe comes after an unknown is presented. A hypothesis is made which is basically a best guess, and even then this comes about with at least a scratch of evidence to support the reasoning in the first place. As I said, simply because you don't have an answer or a sufficient answer to unanswerable questions, like what is our purpose, this does not actually mean there is a god. An unknown is an unseen nothing more. You say 'some other process must be involved'. Okay, I agree. Sure. Does that mean it's "God" time? No offense, RF but no. Just because we can't see it doesn't make it something. It's null.

People have to do this though, including scientists/researchers. People must insert a best guess in place of any unknown. It is our flaw and our greatness. We are very very good at pattern-matching, but we also have to do it even when we 'cant' in order to understand our world. We look up at the sky at night and we do not know what we're looking at, but we must always put an answer there so the god's made it...a canvas of night with pin holes, or whatever. It is not enough to simply not wonder about it We can't do that. We can't not presuppose, then construct, and then think we know.  It always seems obvious too that the things we can't explain means there "must be more to it all". Well yeah. There is, so lets keep looking.


Ahk

It is interesting that RF is ignoring COS, who has responded with scientific, not scientistic, answers. Its a shame that Creationists simply refuse to see real science and focus on propaganda.

I would urge you to recheck your information.  You are speaking no doubt of the work of Morgan to establish the chromosome theory of heredity.  However it was much later in the seventies that Edward Lewis showed how mutations in the developmental regulatory genes often had bizarre effects including flies with four wings or flies with legs sprouting from their heads where antennae should have been.  These "homeotic" mutations were formed by very minor mutations that caused big mix-ups in the body plans.  However these mutations do not involve new protein bindings they are a result of developmental control genes that coded for proteins that in turn switched other genes on and off.  These are now called the hox proteins.  Further work uncovered a large number of cascading control genes and proteins that when altered would cause no end of mix-ups.  But none of these changes address the kinds of difference observed between Chimps and humans and none of them explain alterations to body parts.  In fact substitution of the gene that controls eye development in a mouse when inserted into a fruit fly in the antennae control region causes a fly eye to grow on the antennae but not a mouse eye thus confirming that these are indeed control switches.

Morgan was working (among other things) on how fast do mutations develop, what are the consequences of mutations, where on the chromosome is the cause of mutation. The DNA and protein level of his experiments was explained later.

A typical gene regulatory protein has 2 domains. A DNA binding domain and kinase domain (that interact with protein). A gene is switched on/off either by mutation in DNA binding domain (won't go into details as you are interested in protein:protein) or by mutation in kinase domain. Now mutation in this region does not necessarily cause on/off. It can also result in changed affinity with binding protein (resulting in over expression or lower expression of gene regulated by this protein), or that it binds with a different protein altogether. So yes, there is a changed/new protein:protein interaction.

An even better example is sickle cell anemia in human medicine (but I left this one out, because the initial mutation was not observed in the laboratory, for obvious reasons). One single nucleotide mutation in one of the globin genes changes amino acid sequence in the protein, causing to fold differently, causing to interact with other protein components of hemoglobin in a different way, causing multiple haemoglobin to bind into a cristal structure, interacting with components in the cytoskeleton and on the cell surface to misshape the cell. A whole bunch of new protein:protein interaction from one single nucleotide change.


In know people are often frustrated why fundamental genetics is done on flies, E.coli and mice. There is a very good reason... ethics.


RF is not ignoring me, we have discussed this issues several times before. From my perspective, it is difficult to find simple examples to explain them to forum members. For RF, he tried to explained me in details about ID, but we ended that debate on weather a cloud in the shape of Austria is complex enough or not. It's the criteria of what is complex enough and what not that I don't accept from ID.

About real science vs propaganda vs religion, I am sick of that subject.

Very good, then, I will take my leave. I am enjoying your explanations and find it frustrating that for all RF claims to have settled on ID as a better explnation, he seems to refuse or ignore the actual science and only takes the Discovery Institutes version of science.

Keep up the good work. I'd love to hear more.

I second this COS, I am fascinated by your explanations.

Yes, thank you tejtej.

Very informative.

[applaud]

Again I would ask you to recheck your information.  Can you provide a specific example of a new binding site or are you only speaking of changes to existing binding sites resulting in changed binding affinities as you indicated?  Evolution has demonstrated that it can change and in the process break existing function including over and under expression of regulated genes and the out of order expressions I described earlier.  I have asked specifically about new binding sites and new interactions.


Actually this is another example of a change but not in a binding site but rather in a folded area that normally prevents the heme portion of the mutiprotein hemoglobin to contact other areas of the structure that have modest affinity to it and also to other heme structures that are otherwise also protected but only when the heme is not bound to Oxygen.  The result of the change is that existing (unitended)  binding sites are exposed, but these are not new binding sites.  More importantly is the impact of this change.  This change causes the hemoglobin to form up into a gelatinous mess and alters the entire shape of the blood cell causing it to clump in capillaries when the heme is not bound to oxygen and more importantly the spleen recognizes that these cells are deformed and destroys them leading of course to anemia.

The primary point is that this change in the fold only exposed otherwise protedted heme causing a major misfuntion.  These areas that are now exposed existed already.  They are not new.

So do those of you who see the kinds of examples offered as valid indicators of ability to generate the actual observed differences?  Do you believe these examples are "close enough"?

I ask this because if these examples did represent the mechanisms the generated new protein protein interactions and since these single step mutations are relatively frequent (1 per 100,000 base pairs) why is it that the examples are so sparce and why is it that we can't identify even one example of a mutation that exposes a previously concealed potential binding site that builds useful new function?  In other words, why does the narrative not match observation?  


Did you misunderstand? The bizzare effects demonstrated with mutations to regulatory control genes in fruit flies are not in the same category of differences as those between apes and humans and therefore do not offer a solution to the issue I have raised.  They represent changes in control function that dramatically messes up normal developmental function.  They are not new proteins, new protein binding sites and new protein function that make up the differences in expressed genes that this article and this discussion focuses.


Actually I agreed that a cloud shape is absolutely complex enough.  My point was that the shape could not be specified inependently from the event prior to the actual stipulated occurance.  It was not detatchable in that we cannot say that we regularly observe clouds in the shape of countries. The marker for design requires complexity and specification but the cloud represents only complexity.

RF, give me a few days for an answer.

Specification of what? It seems that in this case you are only judging it against a known design that you recognize (not the process of design itself - which ID has not determined or defined).

That is, you say it hasn't distinguished itself apart from its process, but this is exactly what evolution is.  So, again, how do you determine that life "appears designed" when you have nothing in the process to point to as outside of its natural progression?

I started a new thread "specification and Design" to answer your question, barney.

I'll try to answer most of issues together.


Hm.... So what is a "new" binding site. I would say that a non exposed region is not a binding site as nothing can bind to it and it is not under selection pressure for any kind of binding. It a newly exposed region has something to bind it it is a new previously non existing binding site, subject to a new previously non existing selection pressure.


In so closely related species as human and chimp most changes are in the affinity (a lot of examples in "fine tuning" of gene expression), simply because time from divergence has not been long enough to make a big leap. Given the time available, there is no way that in one of these two an insertion of about 150 bp (which would code 50 amino acid (aa in the rest of the text) long section, a reasonable length for a new binding domain) would accumulate trough mutations. As you mentioned, mutation rate is about 1 per 100,000 base pairs, estimates for eucariotes are somewhere in that order, or even 1 per 1 000 000, per generation. But consider that insertion is a less likely event than nucleotide substitution, that less than 2% of genome is protein coding, a third of mutations in coding regions are silent because of redundancy of genetic code and a majority of mutations don't get fixed in population. That a new section of one gene coding a totally new binding site (not duplication, not changed, not duplicated and changed) would appear in such a short time... no, I can't find a specific example of that.

For genes involved in basic metabolic pathways and, any new domain is unlikely. Example: human myoglobin (154 amino acids) differs from sperm whale myoglobin in 25 aa, and in 88 when compared with shark myoglobin. Now 500 million years separates humans from sharks and still our myoglobin has no new binding domain in spite of aa changes. Selection pressure, myoglobin has a job to do. There is a twist in myoglobin evolution which I will explain later.

Now the genes that are subject to more quicker evolution are those involved in "fine tuning", that is regulation of DNA expression, in immune system and cell to cell communication. A typical genes from this group are usually code proteins with names something like:

• [insert name of protein]-like protein
• hypothetical protein, similar to [insert name of protein]
• cell surface receptor/antigen
• [a name for a short DNA sequence]box binding protein

and so on. In this type of genes, a minor change in aa sequence can change the pattern of protein-protein and protein-DNA reaction. Protein-DNA interaction can be followed with several variants of microarray experiments where changes in expressions are monitored across thousands of genes spotted on a small piece of glass. Small changes in aa result for example in 200 genes to be upregulated, 200 genes to be downregulated. Protein-protein interactions and how they are changed are not studied beyond individual cases, because there are no cheap systems available to monitor them. There was a total protein-protein interaction map done on S. cerevisiae (yeast), but they only have 3000 or so proteins. Human 20000 or so genes code several times of that proteins, that further modify each other in mature forms. So one would have to check binding of 1 protein against at last 1 000 000 other proteins. Not possible with current technology.

New protein-protein interactions via new binding sites (totally new, not just changed affinity) are monitored only trough comparing some more researched enzymes of distant organisms. A classic example is DNA polymerase. In procariotes, it is very simple, in eucariotes, it binds with a bunch of other proteins (activators, inhibitors, helicases, gyrases....). So here you are, totally new binding sites on the DNA polymerase core protein evolved to interact with other proteins.

Of course, such a distant comparison is problematic, as it can only deal with proteins available in both organisms and because of great differences in generation time in both organisms. Currently, there are not a lot of organisms between mammals and procariotes with finished genome sequences (I can think of chicken, 2 fishes and fruit fly - hm, is it still the only invertebrate?). Comparisons between them and human has only recently begun.

To avoid distant species and different generation time, a detailed globin family study was done to monitor "evolution in progress" as my Biochemistry book by Mathews & van Holde says. Now euchariotes have much lower rate of mutations than procariotes and longer generation times (E. coli - about half an hour, human - 20 years or so). So most evolution in eucariotes was done by small changes with big consequences in gene expression (see microarrays experiments) or by duplications of individual domains (like transmembrane chains, kinase domains...) or duplications of whole genes. This duplications have the advantage that from the pair can maintain previous function, while the other can evolve with no fear of strong negative selection pressure. Exon-intron organisation of eucariote genes seem to enable such domain duplications, while mobile elements like transposones can copy paste section of genes or whole genes. When monitoring evolution of such a gene in a single species, generation time and mutation rate is a constant.

So, gene coding ancestral globin diverged trough gene duplication 800 million years ago (estimates obtained when comparing organisms that diverged previously) in myoglobin and hemoglobin. Myoglobine can is a single chain protein holding one heme group. Hemoglobin evolved further as 500 million years ago when it was duplicated into alpha and beta chains. These developed new binding domains that enabled them to form a 2-alpha chains, 2 beta chains and 4 heme groups protein. These binding domains are not present in myoglobine that is incapable of binding with other globins. But most of differences in genes/proteins in human (at least 9 functioning globin variants and a bunch of fast evolving pseudogenes) is in affinities, time of expression of globin and tissue where it is expressed. This is where diversity of higher organisms, like mammals, comes from.

I'll address each item separately and return to your other response later.


Let's stay focused on what we can know and infer through empirical studies.  I recognize that "what-if" analysis has its place but this topic is about what we have learned about evolutionary processes through observation and experimentation.

Your hypothesis is that new protein-protein binding sites are formed by exposing previously existing protein structures when relatively simple mutations change the physical shape of an existing protein.  You offered an example, the sickle cell trait which is known to dramatically reduce both the capability and function of hemoglobin and the red blood cell by causing hemoglobin to form into a highly disorganized (and very high entropy gain) tangle of gelatinous muck.  It forms the kind of structure one would expect from a random event that breaks normal function.  It is similar to the effect a tree limb has when falling through and shattering a window. 

Contrast this with the prototypical protein-protein interactions.  I offer this site to better illustrate what I am describing.

Protonic NanoMachine Project from Japan Science and Technology Corporation (http://www.npn.jst.go.jp/)

I urge you to look carefully at the illustrations, and the movies and animations to understand the inherent structure involved in functional protein-protein interactions and contrast them to the example you offered.  Clearly empirical observation of functional protein systems confirms that your example is not in the same class.  Your example instead falls in the category of all other observed evolutionary changes that break current function and destroy or damage orderly operation.

Wherever molecular biologists peer into the nanoscale workings of biological systems to observe protein-protein interaction, they find systems similar to the animations I provided.  They do not find random nonspecific shapes like the sickle cell trait you described.  Perhaps you can offer an example of a modest change exposing a pre-existing structure that is part of a structure of well fitted and functional protein machines or systems like what we actually observe in real and functional biological systems.

Please avoid this term.


Mutation causing sickle cell anaemia is not breaking current function (transport of O2) or destroying orderly operation. It is a new adaptation in host to pathogen relation and is currently under positive selection pressure.


I don't understand. Please rephrase the question.

I see what's happening in the subject lines of tejtej's posts I'm going to assume it will stop since Im going to find out who it is.

That would be me (full of it). It was my subject line.

You edited it like that? OK. I thought for a moment people could get into other posts or something. Thanks for clearing it up.

Inherent as in intrinsic.  You find fault with my word choice?


I am surprised you deny that sickle cell anemia represents broken and reduced operation.  Part of fit for purpose operation is the systems ability to co-exist with wider operation.  In the case of sickle cell, the defective protein (it is considered a defect) results in collapse of the normal red blood cell shape causing the spleen to interpret that the cell is damaged and target it for destruction, thus the anemia.  Surly you agree that those with this condition are impaired.

However as  you indicate, the sickle cell trait is an excellent example of what evolutionary processes are capable of accomplishing.  In the process of reducing (breaking) functional capability of the red blood cell system, this trait also provides a degree of protection from the malaria parasite by disrupting its life-cycle.  When those who have one sickle globin gene and one normal globin gene, oxygen carrying capacity is reduced slightly but the cell does not collapse to the same extent and the spleen does not destroy the cell.  However when malaria is present in the cell, it is much more easily damaged and also collapses so that the spleen now targets infected cells while preserving the relatively more healthy cells.   Once again this is an example of evolution breaking or damaging normal function in order to preferentially target a larger threat that is applying selection pressure.  Note that genetic studies in America and Europe indicate that where the pathogen is removed, this weaker trait, no longer be selectable, is in decline verses more functional globin.  There is no indication of a permanent path forward.  What is interesting is that there are numerous other mutations with similar effect (various forms of thalesemia) that also cause a weakened infected blood cell also preferentially destroyed.  Each one of these is also considered a defect, et each also makes malaria more survivable.  None of them show any sign of further progression.  None of them show any ability to become better at fighting off malaria.  More to the point, it is this accident which involves damaging function that has proven valuable in surviving malaria and yet the system in our body who's purpose is to identify and eliminate pathogens has proven useless and incapable of evolving any functional defense against malaria.

Returning to the primary point, this example is not in the same class as the well fitted protein-protein binding interactions we observe throughout molecular biology.  I urge you once again to have a look at what we actually observe in biological systems.  Protonic NanoMachine Project from Japan Science and Technology Corporation (http://www.npn.jst.go.jp/)


I'm sorry for the confusion.  Can you find an example where a binding site is exposed and the modified protein is used in a structure similar to the flagellum or cilium systems described in the link? 

I don't recall the term from any paper, which means I have to search for a dictionary only to come to conclusion that it's a philosophical term.


Heterozygous people have the advantage. Potentially it is not an evolutionary dead end. Perhaps just a tiny change in regulation of haemoglobin digestion is needed to form a negative feedback control that would prevent clinical symptoms of homozygous people.


Nice web site. My boss is urging me to include movies and a blog on our site.


I know you are fascinated with flagellum, but I fail to see what makes it so special. Self assembly of monomeres or other smaller molecules into complexes is a very standard process.

I insist that change from myoglobin to hemoglobin that enables binding several hemoglobin chains into one complex and hemoglobin in sickle cell anemia are good examples. But unlike in other self assembly processes (formation of flagellum, fibres that separate chromosomes in mitosis, muscles from actin and myosin) the later example is a process with no apparent breaks.

When you begin to speculate you leave the realm of empirical science.


It is not the fact that complex self-assembly by regulatory control circuits, inventory scheduling and management, component transport and assembly control occurs, it is the fact that these are the exact coherent mechanisms used by engineered processes and they don't resemble in the slightest the incoherent processes employed by materialistic mechanisms. We know of no materialistic mechanism that works this way. When we peer into the nanoscale of cells we observe processes that are uniquely characteristic of design. 


Trouble is you cannot use empirical science to demonstrate that myoglobin changed into hemoglobin.   You cannot demonstrate that the Ha and Hb binding sites that create the required tortion to expell oxygen in depleted zones happened by chance.  We have nothing from observed evolutionary processes to indicate that these coherent systems can be constructed by stepwise change.  Experimental biology is showing us what evolution can accomplish and more importantly what it cannot accomplish. Evolution can derive sickle cell trait from hemoglobin protein b. We can demonstrate that because we observe base pair substitution.  But that seems to be near the limit of what evolution can do.


I would be interested in a detailed description of each potential step that may have went into generation of these systems by evolutionary processes.

RF said:


I would be interested in any identified design process or event.

Genetic engineering provides a number of design processes that apply making genetic alterations.  Unlike evolutionary processes these design processes add new functionality very quickly.

Can you provide an example of a new binding site anywhere throughout the entire span of organisms?  If we include your hemoglobin example (I will return to that one) I know of two.  The second is FKBP.  But a typical cell includes about 10,000 binding sites.  The FKBP example is also one of binding with itself when a substitution at position 36 causes the protein to bind to itself with moderate strength (about 100 times more strongly than sickle hemoglobin).  In a paper by C. T. Rollins and a host of others, in 2000 Proceedings of the National Academy of Science - USA , they make the strong point that this is unprecedented and appears to be the reversion of a previous mutation now being undone so strong is the affinity and natural is the fit.  It was as if the protein was engineered for the fit created.


Fit for purpose prevents change over time indeed.  This similarity could be common descent as you presuppose or it could be reuse of intentionaly designed components.



Isn't this just an excuse?  It sounds like the complaint, "I just need more time to find the missing processes and new interactions".  The reality is that we have studied or had the opportunity to study 10^30 organisms to uncover new binding sites and we have not found any good examples of a new one like the 10,000 we find in each cell.  But by the odds and compared to the rate at which these interaction need to be occurring in order to account for diversity by evolutionary processes, we should have discovered several thousands by now.

See above, DNA polymerase in procariotes and eucariotes.


By far the most important excuse is that I am microbiologist and not really good at mammalian examples.

Where is your evidence? Genetic engineering analagous to human endeavors requires advanced technologies. What did the designer(s) do? Snap their fingers? Given the obvious progression of life on earth what other explanation can you offer other than descent with modification?

These examples don't seem to be observed, or repeated in experiments.  Can I assume they are presumed or Inferred?  I don't understand how biologists feel justified in suspending the scientific method.  I am aware of the speculations.  I was hoping to understand what has been confirmed.

Essentially, you don't like some examples because the new binding site is not "new" (it is) and other because they include organisms with millions of years since divergence.

De gustibus non est disputandum.

Fair enough.  I will accept the sickle cell Hb example for now and we can look even closer at it and its characteristics.  Surly you admit that this example is nothing like the examples of the thousands of functioning binding sites we actually observe in a properly operating cell.  The nanomachine site I offered earlier provides a glimpse into the functional binding sites of which I speak.

Speculations separated by millions of years are not consistent with the requirements of the scientific method and are not causally sufficient.  We observe similarities and we can even speculate that one was derived from the other, but we cannot say how it change took place.  It is pure speculation to claim evolution did it when experiments seem to indicate evolution cannot do it.

Sickle Hb is a special case of protein-protein interaction.  The interaction that is exposed by by the substitution is weak as compared to the interactions one encounters in fully functional protein machines.  It is nearly one hundred times weaker than the typical binding locations and its dissociation constant is quite high (Ivanova, M., et al., 2000,  Nonideality and the nucleation of sickle hemoglobin, Biophysics Journal).  The only reason it has the effect it does is because the red blood cell unlike nearly all other cells has nearly 90% of all its protein content as one protein, namely hemoglobin.  This high concentration compensates for the weak association and allows the hemoglobin to congeal into an incoherent web of gelatin in contrast to the protein interactions one encounters in functional systems.

Clearly the difference between sickle hemoglobin and all the others is stark.  It is clear that this is a case of an accident as we all acknowledge mutations are.  The others have the strong appearance of intentional design and we have yet to observe how unintentional constrained chance process can build coherent systems when the overwhelming number of permutations are incoherent (systems of proteins involve permutation in the range of 10^50 to 10^40000).

Considering that protein-protein interaction are difficult to study (=expensive and time consuming) most of studied interactions are special cases. Except antigen-antibody.

Just asking, but why did you focus on protein-protein and not protein-DNA?

True enough, but I'm not sure we are using the term in the same sense.


I used it because the examples seemed easier to illustrate than the gene and regulatory control examples and because the context seemed easier to describe as well.  When we deconstruct developmental control systems they look as much like electrical control circuits and logic as any of the control systems I've built for process control  so I am happy to entertain them as well.

Either way the conclusions is the same and that is that modification by evolutionary processes along with natural selection are not observed to build the kind of systems we find when we peer into the functioning cell.  Instead we find evolution damaging coherent funtion, generating incoherent byproducts and only preserving these changes when selection pressure is such that the damage also disrupts an even more damaging system

Antibody - protein, antigen - for example foreign proteins.


"Damaging coherent function" is a relative term. How about bacteria gaining resistance against antibiotic? Is that a good example of gaining function by mutation?

So what's the subtext to this discussion? That evolution is a myth? That humans were created 4,354 years ago last Tuesday?

No.  The subtext is that known evolutionary processes can't account for the changes we observe between even classes, orders, families, and generas

except that they can, but that is neither here not there for the religionist on a campaign to burn science on the pyre.

Yes, he is also convinced that everyone but he misunderstands the chemistry behind the origin of life, and all their Ph.D.s are but a piffle.

Here's a snippet from a texbook that RF referenced in the SETI thread:


But I must admit, RF is one of the most curteous posters I disagree with.

You can demonstrate with empirical evidence that your statement is true?  You and I both know you cannot.  You have presupposition, a narrative, a few boxes of similar looking fossils, and some similar genes and DNA strands and that is it.  But even the fossils and DNA are not evidence of your claim since neither tells us anything of how they came to appear the way they do.  Sorry barney the scientific method demands more.  Observed evolutionary processes have not demonstrated that they are capable of generating the large quantities of new biological information required to transform a community of organisms into a new genera in the timeframes indicated by the presumed life-span of this planet.  Perhaps you can tell me how evolutionary processes generate new biological information.  Next you can tell me what rate it does so.  No you can't answer these questions either.


You seem to have a bad habit of presuming and ascribing beliefs to your opponent.  I have not made this claim and do not agree with it.


I do not disagree with the words quoted here either.  I am quite aware that microorganisms are evolving in response to drug selection pressures.

You can demonstrate with empirical evidence that your statement is true?  You and I both know you cannot.  You have presupposition, a narrative, a few boxes of similar looking fossils, and some similar genes and DNA strands and that is it.  But even the fossils and DNA are not evidence of your claim since neither tells us anything of how they came to appear the way they do.  Sorry barney the scientific method demands more.  Observed evolutionary processes have not demonstrated that they are capable of generating the large quantities of new biological information required to transform a community of organisms into a new genera in the timeframes indicated by the presumed life-span of this planet.  Perhaps you can tell me how evolutionary processes generate new biological information.  Next you can tell me what rate it does so.  No you can't answer these questions either.


You seem to have a bad habit of presuming and ascribing beliefs to your opponent.  I have not made this claim and do not agree with it.


I do not disagree with the words quoted here either.  I am quite aware that microorganisms are evolving in response to drug selection pressures.

how fast are they evolving? Or, anytime intelligence is involved (e.g., drugs), you get to declare it not applicable?  Do other organisms include in this subset, since you presume they were designed by God, you must conclude that even things evolving far from man's reach are ID'd... and on it goes...

Again I do not disagree.  These interactions though do not occur by evolutionary processes and this is why I say they are not the same sense.  They are managed by a series of finely tuned nanobots that effectively search shape space and chemical affinities to result in identification and generation of specific proteins with appropriate binding sites.  Remarkably designed mechanism that totally defies a materialistic explanation.


I don't think so.  When we look at specifically what is going on, we don't find new functionality.  Instead we find that preexisting function is damaged and in the process the bridge or key that used to allow the antibiotic to exploit a vulnerability has been blocked or the keyhole has been filled with gum so to speak. 

Yes, that is the question I ask.


No, selection pressure is selection pressure regardless of the source.  At what rate are parasites, bacteria and insects evolving in response to the selection pressure of drugs and chemicals?  Experimental analaysis shows it is not very fast and not very far.  But don't take my word.  Research it and then tell me, how fast is it?


Show me any organism you wish and tell us what rate is it evolving?

In this the question about drug resistance?

We have done this in microbiological practicum. A culture of E.coli is divided in half. One half goes on a first petri dish with antibiotic (kanamycin or ampicillin, I forgot), the other half goes under a UV light for a minute or so and then on a second petri dish with antibiotic. Overnight incubation -> first petri dish is clean, no bacteria survives. The second has a few colonies.

Without such mutagens like UV, mutation rate is somewhere between 1 nucleotide in 10 000 and 1 in 1 000 000 per generation. E. coli has about 3 500 000 nucleotides, generation time about 30 minutes, number of cells per milliliter of liquid media about 100 000 000. This is about how fast they mutate not about how fast these changes are selected (=how fast they evolve).


The speed of evolution is not a constant value. The speed of evolution of genes in the same organism is not a constant value.

Thank you tej, that was interesting.  Your job sounds fascinating to me.  And thanks for pointing out that the restatement barney offered was vague, I should not have accepted it. That was my fault.  I was asking about selection.  Specifically I was challenging those who view drug resistance as good examples of how evolution accounts for observed diversity to estimate the rate that these evolutionary processes are generating new biological information, the kind required for new form and function.


Fair enough.  I should have asked for an average over an observed period.  I also once again intended to ask about accumulating new function and the corresponding new biological information.

Some genes seem to have almost zero changes among all organisms compared, like histones in eucariotes, molecules that hold the DNA. And some seem to evolve very fast. At the 1. FEMS congress there was a presentation about comparing genomes of different strains of E.coli. Whole sections (up to the third of the genome) were different (or present/absent), mostly genes involved in host:pathogen interaction. How to tell at all if this functions were gained from a simpler ancestral E.coli or lost from a more complex ancestral E.coli?

Right, It appears that some conserved proteins are critical for biological function in many organisms.  Any modification of these genes cause failure so they don't carry forward.  Other sections of the genome are not critical and are subject to modification without significant effect.  It is consistent with my original premise that you would see evolutionary modification in genes involved in pathogen interaction since these pathogen pathway blocking techniques that damage or degrade function but block out the even larger threat seem to be one thing evolution is quite proficient at accomplishing.

Returning to your previous example of bacteria exposed to (high energy) UV radiation which is also known to damage genes should have a similar effect.  UV is completely random in its damage and some of the billions of organisms will have just the right genes damaged to block the antibiotic pathway but still allow the weakend bacteria to survive and duplicate in an environment now free of competition.

These are all good examples of the evidence that evolution damages function to block pathogen and damaging chemical pathways but does not seem to build new function.  If evolution also built new function we would predict the conserved genes to also show evolutionary characteristics and also they should be identified as sources for evolved genes but they don't. 

Once again analysis from probability provides the basis to explain why we don't see behavior.  Evolution can and does successfully mutate to alternate functional forms when the probability involved in the alteration is greater than the inverse of the number of probabilistic resources available (organism count is the primary resource) but does not when the probability involved in a new or alternate functional protein is less than the inverse of the resources.  Bacteria counts on this earth are estimated at 10^35 or so but the probability of obtaining a functional protein from random change is less than 10^-55 for even the shortest ones.

Going in circles.


Explained when I compared flagellin to a human protein with a different function.


Again the subjective "what is a new protein". Under UV a functional protein able to digest (or avoid) antibiotic can be produced in minutes from a protein that lacked this ability.

Indeed.  We have a different view about what counts for evidence for a pathway.  You seem to count the outcome as evidence of a specific path, but the outcome is explained by many possible paths.


By this I take it to mean that the reason we don't observe the expected behavior is because it is obscured by the large number of posible pathways and potential starting points in attempting to recreate history from a narrative.  Instead let's stick with what we can and do observe and test.  We observe mutations occuring and we even know how to accellerate mutation rates, but we don't observe a progression of changes building on each other to produce new functional components.


Have we confirmed that these protiens have new function with no loss of old function?  My understanding is that function is lost (or reduced) and in the process the antibiotic pathway is also lost.