Anti-malaria drug resistance requires at least two mutations

wd400:

Behe’s argument (which is flawed) applies only to cases where intermediate sequences have no (or bad) fitness consequences, and specific changes are required in a single gene.

Simply false. The Edge of Evolution: Why Darwin's Mechanism Is Self-Limiting Mung

The Edge of Evolution: Why Darwin's Mechanism Is Self-Limiting - Michael Behe - July 18, 2014 (Part 3 of 3) Excerpt: As science probes ever deeper into the molecular details of life,, grave obstacles to undirected evolution have become manifest. Relatively recent, terrific research using the powerful techniques available to modern biology shows three general, separate barriers to a Darwinian (or, for that matter, to any undirected) evolutionary mechanism. (1. random mutation, 2. natural selection, 3. irreducible complexity),,, It's important to notice that these three roadblocks are substantially independent of each other. Sequestration of a system to its current function by natural selection is a different problem from the damage done by adaptive-yet-degradative random mutations, both of which are conceptually distinct from the need for multiple, unselected steps to reach some adaptive states. A result of their independence is that they will work synergistically. Undirected evolutionary change faces multiple overpowering restraints.,,, http://www.evolutionnews.org/2014/07/the_edge_of_evo087971.html bornagain77

As to wd400's usual denial of evidence, I would like to add a few points. First is the fact that the modern synthesis, which wd400 holds as true, is now known to be false. As Dr. Nobel succinctly puts it:

“The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences

A few more notes along this line:

“Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.ncbi.nlm.nih.gov/pubmed/15888340 In Embryo Development, Non-DNA Information Is at Least as Important as DNA - Jonathan Wells - May 2012 Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns. http://www.evolutionnews.org/2012/05/in_embryo_devel060031.html Not Junk After All—Conclusion - August 29, 2013 Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. https://uncommondesc.wpengine.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/ etc.. etc.. etc..

Thus, regardless of whatever wd400 may claim to the contrary, the plain fact of the matter is that he is working from the wrong theoretical foundation in the first place. The cell is best viewed holistically rather than from a 'bottom up' reductive materialistic approach. For wd400 to claim otherwise is for him to put his materialistic philosophy ahead of what the empirical evidence is clearly indicating! The second point I would like to bring up, that undermines wd400's materialistic worldview, is 'context dependency'.

(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

Moreover, context dependency is found on at least three different levels of the protein structure:

“Why Proteins Aren’t Easily Recombined, Part 2? – Ann Gauger – May 2012 Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.” http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2

Moreover, many (most?) proteins are now found to be multifunctional depending on the overall context (i.e. position in cell, cell type, tissue type, etc..) that the protein happens to be involved in.

The Gene Myth, Part II - August 2010 Excerpt: "Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent." Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy Metamorphic Proteins - 2008 Summary: Proteins that can adopt more than one native folded conformation may be more common than previously thought. http://www.sciencemag.org/content/320/5884/1725.summary Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013 Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.” http://www.fasebj.org/content/23/7/2022.full

Context dependency, and the insurmountable problem it presents for ‘bottom up’ Darwinian evolution is perhaps most dramatically illustrated by the following examples in which ‘form’ dictates how the parts are used:

An Electric Face: A Rendering Worth a Thousand Falsifications – Cornelius Hunter – September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” https://www.youtube.com/watch?v=wi1Qn306IUU What Do Organisms Mean? Stephen L. Talbott – Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements … take unique meaning from their context.[3]“,,, http://www.thenewatlantis.com/publications/what-do-organisms-mean

Of course, much more evidence could be brought against wd400's position. But for now, it is good for the uninitiated reader to know just how detached from reality wd400's claims actually are. bornagain77

Behe appears to have taken this number from a statement in a paper, which is not supported by a calculation or a citation. I see now easy way to get from "rate at which we observe a phenotype" to "rate at which mutations arise" that doens't include a list of assumptions about the strength of selection, exposure to the drug and the rate at which Plasmodium moves from patient to mossquito so I think it's a bit rich to call it an empircal fact. Behe's argument (which is flawed) applies only to cases where intermediate sequences have no (or bad) fitness consequences, and specific changes are required in a single gene. So it's not true that he'd argue 4 or more sequential changes were impossible (perhaps this is what you mean by co-ordinated?) wd400

Wd400 - because the empirical evidence suggests it? Chloroquine resistance occurs at roughly that rate and necessitates 2 coordinated mutations which is what the maths predicted which is the whole point of this thread. What observable evidence do you have to believe that the probability is unlikely to be that for an average sized protein? I should have written 4 coordinated mutations or more are impossible by probability not 3. I.e. 2 sets of coordinated mutations. Rhampton - yes that's the point - due to population sizes the resistance can be accounted for by natural random mutations. But if you required more than 1 set of coordinated mutations to occur, no organism could realistically achieve that given the estimated age of the earth. Dr JDD

Dr JDD, You say this is a case of micro evolution that "happens at a rate of around 1×10^20". Do you think any natural mechanism can account for Anti-malaria drug resistance? rhampton7

Yet 2 sequential/coordinated mutations are required. And that happens at a rate of around 1×10^20. How do you know this? However, we are to believe that the components of a cellular pathway (KREBs cycle, complement pathway, ATP synthesis, etc, etc) does not require mutational events that necessitate > 2 sequential changes? No Even Behe doesn't claim that pathways requiring > 2 sequential changes are unreachable. wd400

Let us be clear about something. What we are talking about here is micro-evolution. I repeat, this is not a large jump this is merely losing the ability for a drug to bind to a protein thus conferring resistance. There is no novel function gained, no new cellular processes or pathways derived. Yet 2 sequential/coordinated mutations are required. And that happens at a rate of around 1x10^20. However, we are to believe that the components of a cellular pathway (KREBs cycle, complement pathway, ATP synthesis, etc, etc) does not require mutational events that necessitate > 2 sequential changes? Further (as those processes are more realistic with bacterial numbers), the complex genes involved in body plans seen in the animals such as in the Cambrian explosion - are we to accept that these could occur in that short time frame with all those necessary protein components on all <3 sequential mutations from pre-existing material? Really? Yeah that's right, IDers are the ones who aren't using their brains, honest guv. Dr JDD

OT: New Paper in Bio-Complexity: How the Burgeoning Field of Systems Biology Supports Intelligent Design - July 2014 Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems: *"Negative feedback for stable operation." *"Frequency filtering" for extracting a signal from a noisy system. *Control and signaling to induce a response. *"Information storage" where information is stored for later use. In fact, Snoke observes: "This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. " *"Timing and synchronization," where organisms maintain clocks to ensure that different processes and events happen in the right order. *"Addressing," where signaling molecules are tagged with an address to help them arrive at their intended target. *"Hierarchies of function," where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order. *"Redundancy," as organisms contain backup systems or "fail-safes" if primary essential systems fail. *"Adaptation," where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, "These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way," and "Only part of the system is allowed to vary randomly, while the rest is highly conserved.",,, Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that "just about everything in the cell does indeed have a role, i.e., that there is very little 'junk.'" He explains, "Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible," and quotes additional authorities who assume that biological systems are optimized.,,, http://www.evolutionnews.org/2014/07/when_biologists087871.html bornagain77

"Any theory who’s sole tactic is to poke holes in another theory, without presenting a reasonable and testable alternative, is doomed to failure." Tell that to the iceberg that sank the Titanic. OldArmy94

wd400- In what way is 21st century evolutionary biology different from Darwin's theories? Did someone come up with a new designer mimic or is natural selection still the only mechanism capable of producing designoid features? Joe

Acartia_bogart:

Any theory who’s sole tactic is to poke holes in another theory, without presenting a reasonable and testable alternative, is doomed to failure.

You have just described evolutionism. Nice job. Joe

So, you’re saying that NS was completely unable to do anything to make the malarial parasite survive: i.e., it could do nothing at all to make the parasite “fit.” Once it was ‘fit’ enough to survive—all this done without the help of NS—then, and only then, could NS help the organism to become slightly more ‘fit.’ NS couldn't make smallpox survive in the face of an eradication program, or mammoths moa or Diprotodon surive the arrival of humans, and it probably want save many other species from climate change. These are not normally persented as evidence that "Darwin was wrong". I don't see how you are getting from "some traits require two mutations, the first of which is not selected for" to that conclusion. Or, for that matter, why we should care since 21st century evolutionary biology is different from Darwins' theories. wd400

AB you claim that ID will not be accepted unless,,,

"all the rational people in the word die"

Pray tell AB, how is rationality grounded within your materialistic worldview in the first place?

“It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”. J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

Myself, I hold that even atheists themselves, when atheists die, will also admit that Design, with a capital D, is all too real:

Romans 14:11 It is written: "'As surely as I live,' says the Lord, 'every knee will bow before me; every tongue will acknowledge God.'"

But sadly, then it will be too late,,, Matthew 10:33 but whoever denies me before men, I also will deny before my Father who is in heaven. bornagain77

"ID will emerge victorious in another 25-30 years when enough young people will have been exposed to the ID argument and the vacuity of the arguments that Darwinists present. It’s a matter of time. There’s no convincing the critics in the meantime." The only way this will happen is if all the rational people in the word die. But it's always nice to have dreams. Any theory who's sole tactic is to poke holes in another theory, without presenting a reasonable and testable alternative, is doomed to failure. Acartia_bogart

wd400: This research shows a trait can only evolve when two mutations are present, and that it is unlikely that either of those mutations produce a fitness benefit by themselves. i.e. , in this case selection only operate when both mutations arise in the same gene. They enumerate other mutational pathways and their likely fitness consequences, which let’s you know how selection will operate once the 2 mutations are in effect. So, you're saying that NS was completely unable to do anything to make the malarial parasite survive: i.e., it could do nothing at all to make the parasite "fit." Once it was 'fit' enough to survive---all this done without the help of NS---then, and only then, could NS help the organism to become slightly more 'fit.' This is just what most IDist would maintain: NS cannot account for jumps in complexity, but once this jump has occurred, it can then tinker and sort of 'fine-tune.' IOW, NS can't get you 'macroevolution;' only 'microevolution.' And, so, Darwin was wrong. PaV

Joe: They will never accept our arguments. The arguments we make are self-evident; if they can deny self-evident arguments, then they can deny anything. It was Planck, I believe, who said that scientific breakthroughs don't occur because one side wins the argument, but because one side of the argument ends up dying. ID will emerge victorious in another 25-30 years when enough young people will have been exposed to the ID argument and the vacuity of the arguments that Darwinists present. It's a matter of time. There's no convincing the critics in the meantime. PaV

So, Michael Behe Was Right After All; What Will the Critics Say Now? - Casey Luskin July 16, 2014 Excerpt: Will Ken Miller, Jerry Coyne, Paul Gross, Nick Matzke, Sean Carroll, Richard Dawkins, and PZ Myers Now Apologize to Michael Behe?,,, Is an apology from Behe's critics then forthcoming? In a world where debates were conducted with the goal of discovering truth rather scoring points, it sure ought to be. Unfortunately, I'm not sure we live in that world. What we'll probably get is nothing more than PZ Myers's concession, offered in the context of the rant quoted above,,, http://www.evolutionnews.org/2014/07/so_michael_behe087901.html bornagain77

PaV- Our critics focus on word-order and anything else they can find because A) they say there isn't anything to debate and B) because to them it proves we are not worthy of a debate in the first place. Joe

That's Behe larger claim, which doesn't seem to be effected by this result as far as I can tell? wd400

...so what about higher organisms not capable of achieving such a population number to produce the chance needed to give multiple proteins that have undergone 2 simultaneous mutations? What about needing more than 2 mutations? Dr JDD

My 'view' on what? This research shows a trait can only evolve when two mutations are present, and that it is unlikely that either of those mutations produce a fitness benefit by themselves. i.e. , in this case selection only operate when both mutations arise in the same gene. They enumerate other mutational pathways and their likely fitness consequences, which let's you know how selection will operate once the 2 mutations are in effect. I've never thought the idea that some traits require two mutations was the major claim Behe was making, but if it is then I'll happily grant. It's true in this case, and there are probably many other traits that couldn't arise by single mutations each with a slight fitness increase. wd400

wd400: What's your view on this? What role does NS play here? PaV

Joe: Confusing the order of the words is a habit that needs to be stopped as our detractors pick up on it and make it seem as if we are dupes. they If our critics focus on word-order, then this is a de facto admission that they have no substantive response. it's child's play. PaV

I think it's the headline for this post and not what Behe said. Silver Asiatic

looks like single mutations in PfCRT do not confer CQ resistance nor CQ transport activity. You need at least the 75 and the 76 mutations for CQ transport activity and an additional three mutations for CQ resistance. Starbuck

... to him! Axel

Can't argue with that, Joe, other than to say that Behe probably said it in his mind with the appropriate stress, as he was writing it - which would have made it clear. Axel

No amount of contrary evidence could be sufficient for members of the Darwin Death Cult. Differential survival rates are The Creator God, period. A God who will have no other gods before Him, Amen. A God who proves His worthiness by being infinitely adaptable, Hallelujah. Whatever it takes... jstanley01

Confusing the order of the words is a habit that needs to be stopped as our detractors pick up on it and make it seem as if we are dupes. Joe

Isn't it a matter of a confusing order of the words, Joe? A clearer order of the words being to have 'chloroquine resistance' follow, instead of precede, 'in malaria'. Axel

Umm the drug doesn't require two mutations. Malaria requires two mutations to ward off the drug's effects on it. [UD. Thx Joe. Title updated] Joe

Behe vindicated in the lab. Many Darwinian critics of Behe's 'Edge of Evolution' proven wrong (yet again): It's Tough to Make Predictions, Especially About the Future - Michael Behe - July 16, 2014 (Part 2 of a 3 part series) Excerpt: The need for multiple mutations for chloroquine resistance in malaria just wasn't that hard to see. So why do you think Darwinist reviewers of The Edge of Evolution missed it? http://www.evolutionnews.org/2014/07/its_tough_to_m2087891.html bornagain77