Fitness effects of advantageous mutations in evolving

1) A few months ago an interesting paper in Science, “Adaptive mutations in bacteria: high rate and small effects”, by the group of Isabel Gordo demonstrated that beneficial mutations in E. coli were more frequent than had been thought. In fact, the authors remark that “We found a rate on the order of 10(-5) per genome per generation, which is 1000 times as high as previous estimates, and a mean selective advantage of 1%.” They show that the previous underestimates of the beneficial mutation rates were likely due to clonal interference — accumulation of beneficial mutations in large bacterial populations which then interfere with each other to dominate the population, making beneficial mutations seem less frequent. Does this new result mean that Darwinian evolution can construct molecular machinery much easier than thought? No. While the result is interesting, readers of The Edge of Evolution will not be very surprised by it. As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems. The bottom line is that the beneficial mutations reported in the new Science paper most likely are degradatory mutations, and so don’t address the challenges outlined in The Edge of Evolution.

"The bottom line is that the beneficial mutations reported in the new Science paper most likely are degradatory mutations..." So who are we to believe? A peer-reviewed article in an actual science publication (the leading such publication in the country), or the opinion of an author of a non-peer-reviewed publication that has been uniformly bad-mouthed in its reviews (except in the religious and right-wing media)? Decisions, decisions...

I am somewhat confused about the concept of degradatory mutations. Yes, in case of malaria, the mutation that provides some immunity also comes at a cost (sickle cell anemia) but in the environment in question, the mutation is hardly degradatory.

I find the logic involved a bit simplistic.
Let's say, malaria goes away, would the sickle cell trait disappear as well? Well there you go, evolution in action once again.

But no worries there are many more papers undermining Behe's 'arguments'

I'm not sure the two results can be compared/contrasted that simply: the units seem different.

What is the conversion factor between "per cell and generation" (cell^-1 generation^-1?); to "per genome per generation"? In the surface: Since we're talking about asexual reproduction, each genome consists of a large number of cells. Or do the authors assume that each cell has an independent genome? I don't have access to the papers... do the authors try to reconcile the two measures?

I don't believe that it would be necessary to use a conversion factor since in any event it is a single cell that must acquire the mutation to pass it on. I do not have the primary source, but my recollection was that there is actually a very a rare third allele that confers malaria resistance and is not harmful like sickle cell, but that because of it's rarity natural selection will not permit it's advance because in hybrid combinations it is less fit than the wild type or sickle cell versions.

Well I believe, as Dr. Behe has clearly pointed out, that stasis is the rule for malaria...as well as E coli and everything else he looked at!

A little more evidence for stasis you may find interesting..

There are many ancient bacterium fossils recovered from salt crystals and amber crystals that have been compared to their living descendents of today. Some bacterium fossils, in salt crystals, dating back as far as 250 million years have had their DNA recovered, sequenced and compared to their offspring of today (Vreeland RH, 2000 Nature). Scientists accomplished this using a technique called polymerase chain reaction (PCR). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost exact DNA sequence.

“Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; (The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes)

http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

Though they do some weird contortions to try to make the evidence fit an evolutionary scenario in their paper,,,just what if the evidence from both Behe and Vreeland (not to mention the law of conservation of information by Dembski and Gitt) is correct,,,High populations of single celled organisms will exhibit stasis. Those are quite a few lines of evidence converging on that fact!

And here is a scripture I was told to give you PvM

ROMANS

1:20 For the invisible things of him since the creation of the world are clearly seen, being perceived through the things that are made, even his everlasting power and divinity; that they may be without excuse.

1:21 Because, knowing God, they didn’t glorify him as God, neither gave thanks, but became vain in their reasoning, and their senseless heart was darkened.

1:22 Professing themselves to be wise, they became fools,

1:23 and traded the glory of the incorruptible God for the likeness of an image of corruptible man, and of birds, and four-footed animals, and creeping things.

1:24 Therefore God also gave them up in the s of their hearts to uncleanness, that their bodies should be dishonored among themselves,

1:25 who exchanged the truth of God for a lie, and worshiped and served the creature rather than the Creator, who is blessed forever. Amen.

1:26 For this reason, God gave them up to vile passions. For their women changed the natural function into that which is against nature.

1:27 Likewise also the men, leaving the natural function of the woman, burned in their toward one another, men doing what is inappropriate with men, and receiving in themselves the due penalty of their error.

1:28 Even as they refused to have God in their knowledge, God gave them up to a reprobate mind, to do those things which are not fitting;

You fail to realize that they are still testing whether or not the bacteria recovered from the Permian salt crystals really are 250 million years or are, in fact, modern contaminants. Scientists are leaning toward the latter, if only because the bacteria are identified as being of the genus Bacillus, which is infamous for being omnipresent in virtually all terrestrial environments.
Of course there is the possibility that those bacteria haven't been fossilized, but, instead, have been literally living within the salt crystals, as there are bacteria that can live in porous and water-soluble rocks.
...
But, nonetheless, how does revived "fossil" bacteria that nearly identical genomes to their modern counterparts negate Evolutionary Biology, and if so, then how come Intelligent Design Proponents still have not been able to demonstrate the alleged descriptive power of Intelligent Design?

it was Ray I believe who insisted on a 100% detrimental mutation rate

WHO CARES?

gees, I can't believe you are letting complete idiots dictate the content of thread contributions at this point.

sad.

Why must we continue tolerate these idiots here?
They don't want to discuss anything, let alone science, in a civilized fashion, they're only out to ridicule and condemn those people who are fortunate enough to not share their smothering stupidity.

Born again:

Explain the origin of the designer.

That scripture in Romans given by bornagain77 is relevant to this discussion only if the writer, St. Paul, was specificially referring to the evolution/creation debate. Otherwise, it is only a useless distraction.

So bornagain77 admits these bacteria are found in salt/amber crystals formed 250 mya.

We are making progess!

That bacteria existed both billions of years ago and today is hardly a disproof of evolution. That sounds like that ludicrous argument I hear over and over, "If man came from apes, why are apes still around?"

ID proponents seem to take seriously Sanford’s concept of ‘genetic entropy’

gees, I can’t believe you are letting complete idiots dictate the content of thread contributions at this point.

Ichthyic got to this first, but I want to pitch in to say that it is probably damaging to fisk every odd concept that creationists Gish gallop in their attack on science. I believe someone claimed in a recent thread that there is one or two mentions of ‘genetic entropy’ on the web. Let it remain so.

Let us concentrate on explaining biology instead. The last part of the post was beneficial, and even constructive. :-P

Well I believe, as Dr. Behe has clearly pointed out, that stasis is the rule for malaria…as well as E coli and everything else he looked at!

And here is a scripture I was told to give you PvM

And rather than quote mining papers, why not read them?
Willing to discuss the findings? Or are you once again embarassed by repeating ignorance?

Title: Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives Author(s): Vreeland RH, Rosenzweig WD, Lowenstein T, Satterfield C, Ventosa A Source: EXTREMOPHILES 10 (1): 71-78 FEB 2006 Document Type: Article Language: English Cited References: 29 Times Cited: 1 Abstract: The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this Manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly From their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the Fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule Out questions of contamination by putatively modern strains.

1:21 Because, knowing God, they didn’t glorify him as God, neither gave thanks, but became vain in their reasoning, and their senseless heart was darkened. 1:22 Professing themselves to be wise, they became fools,

Why must we continue tolerate these idiots here? They don’t want to discuss anything, let alone science, in a civilized fashion, they’re only out to ridicule and condemn those people who are fortunate enough to not share their smothering stupidity.

Ok, while I was prepared to address creationist objections and questions, it seems that there may exist a common confusion as to the relevance of these findings.

Research has found that the distribution of fitness effects of mutations peaks around zero (detrimental) and then has a distribution around 1, with some mildly detrimental and some mildly beneficial ones. I believe that the detrimental distribution is a beta one versus a gamma distribution for neutral/beneficial ones.

Understanding evolution requires one to understand the impact of the MANY parameters involved. Such as population size, distribution of fitness effects, sexual versus asexual reproduction, stable versus changing environment, selective pressures and many more. Unraveling under which circumstances evolution can be succesful and when evolution may 'fail' is important to understanding how the mechanisms of evolution interact with the many additional parameters to understand population dynamics.

Evolution is far more exciting than the simplistic population models we have all grown familiar to. The problem is that many seem to be unable to look beyond them.

Accumulation of beneficial mutations of small effects may allow for multigenetic changes while a single large effect beneficial mutation may sweep the genome. As such, the distribution of fitness effects can be of importance to resolving the issues raised by our critics.
Should we ignore our critics ignorance or help others understand where they went wrong?

PvM

I am somewhat confused about the concept of degradatory mutations. Yes, in case of malaria, the mutation that provides some immunity also comes at a cost (sickle cell anemia) but in the environment in question, the mutation is hardly degradatory.

I don't think Behe is arguing that they are degradatory in the sense of not being beneficial. However, in the manner of being beneficial, they come from destructive and not constructive processes and so won't be helpful for building complex structures.

He doesn't seem to provide any evidence that these mutations are ones that degrade (he just says it seems likely). This doesn's stop him from concluding that they pose no challenge to his thesis.

So bornagain77 admits these bacteria are found in salt/amber crystals formed 250 mya. We are making progess!

— Don Smith, FCD

That’s such a defeatist attitude. Let’s not give more credibility by showing that the concept is wrong.

That’s such a defeatist attitude. Let’s not give more credibility by showing that the concept is wrong.

The whole concept of beneficial mutations as well as their distribution is an essential part of evolutionary dynamics and you seem to be worried about mentioning the term ‘genetic entropy’ and hope it will all go away? Pathetic

I can’t even find the principle of genetic entropy explained in CreationWiki. No wonder it gets ignored.

Bonds the plagiarist was only parroting John C. Sanford who wrote a book titled Genetic Entropy & the Mystery of the Genome in which he uses a version of the very lame 2nd Law of Thermodynamics argument to claim that evolution could not have occurred. Not surprisingly, none of his claims are published in peer-reviewed scientific literature.

Genetic entropy doesn’t exist. That is as far as I got, first sentence.

A recent experiment suggested that if you repeat a flawed argument for any reason, even in the context of refuting it, you tend to reinforce its standing in the minds of your readers/listeners.

Thanks PvM for a decent thread that deals with real science. I for one find this immensely more satisfying than having to continually scroll past the nonsense that spews from the keyboards of such as Pole Greaser. (Has anyone else noted the irony of someone using that name crying about the evils of sodomy?) One of the things that this blog should legetimately do is address creationst arguments. This is not giving them control since we can choose what arguments to address and when to address them. If you don't like this topic move to another thread or another site. I welcome the chance to discuss real science here.

As to the importance of the topic, I completely agree that data regarding the distribution of fitness values for random mutations is critical and that experiments such as these are the proper way to address the issue, at least in prokaryotes. This data is critical for any modeling of the evolutionary process. It should be remembered however, that reality is much more complex that the conditions used in these experiments. I am sure that the frequency of beneficial mutations would be even higher if the environment was more variable. Remember that fitness is not a constant and what is deleterious in one environment can be beneficial in another.

As to the objections by Behe, this guy is obviously no scientist. The results don't conform to your ideas, well just make up some objection and claim it to be true. There is absolutely no evidence whatsoever that all, or even the majority of these mutatins are "degratory". And even if they were, he would have to prove that virtually all of them were exclusively so in order to make his case. And of course, he hasn't even bothered to define the term, so that would be impossible anyway. The evidence is quite clear that evolution can and did produce new structures and new functions using variation produced by random mutations. Trying to claim that it could not is not going to work. Give it up already.

As for the 250 million year old bacteria, of course they are the same as their ancestors in many ways. After all, how much did that environment change? Of course they are different from modern bacteria genetically. Drift operates even in the absence of selection. Gould showed us how long periods of stasis can preserve some features. That doesn't mean that evolution has stopped in these lineages or in any others. As with the other studies, the genetic details reveal the processes involved. Claiming that "bacteria are still bacteria" isn't going to get you anywhere.

And before anyone calls this a strawman, remember that it was Ray I believe who insisted on a 100% detrimental mutation rate.

St. Paul makes an excellent point here about how the religion of evolutionism leads to rampant sodomy...

— Pole Greaser

Pole Greaser,

Sorry for not checking again, but I see that you in fact have answered some of my questions on the other thread, and that you in fact not only disagree with Behe, but accuse him of following the "religion of evolutionism." Now do you plan to (1) say more about the whats whens and hows of your position, and directly challenge Behe and other "kinds" of creationist?

I'm not sure that a broad spectrum average beneficial rate is the best approach, maybe in a first order sort of approach. However it stands to reason that there is going to be a huge variability from one gene to another in terms of beneficial rates. I suppose it is possible for it to be rather uniform, but my intuition is that it should be variable just like neutral and deleterious rates are from gene to gene. Given that some protein architectures seem to be much more flexible (i.e. some common structures carry out many different functions while others have only diversified catalytically into one or two roles). Similarly what about genotype by environment interactions. Is there an appropriate way to categorize the environment in a broad way to examine this kind of effect. Which is to say that by definitions the more different the environment that the mutation rate is being measured in is from the normal environment the more options there are for beneficial mutations. How would one quantify this kind of percentage difference?

Pole Greaser,

I went over your answer again, but aside from disagreeing with Behe, you are still not clear on whether new species arose in-vivo (e.g. by "intelligently directed" saltation) or in-vitro (e.g. by "intelligently directed" abiogenesis). Nor do you say, in that comment at least, whether you agree with YECs or the various types of OEC (e.g. old- and young-life variants). Surely you know they can't all be right.

You wrote: "Where and when are religious questions that science can’t answer."

Science can't provide the infinite level of detail that you and Behe demand of evolution, of course, but surely you can propose some simple tests to determine (1) when the "designs" first appeared in biological systems (as opposed to in the designer's mind) and (2) whether design actuation (aka "information increases") are better explained by an in-vivo or in-vitro process.

Behe lying: “The bottom line is that the beneficial mutations reported in the new Science paper most likely are degradatory mutations…”

JGB wrote:

"However it stands to reason that there is going to be a huge variability from one gene to another in terms of beneficial rates."

I agree. That is one of the reasons why just assuming that all of the changes are "degratory" does not make sense. It would indeed be desirable to do a detailed genetic analysis on all of the beneficial mutations in order to determine what type of gene they were found in, what type of mutation is most often involved, etc.

"Similarly what about genotype by environment interactions."

Exactly. That entire issue is completely ignored. And since fitness is always measured relative to the environment, that would seem to be a significant problem. The experiment could be repeated under changing environmental conditions and the results could be compared. Of course that would complicate things tremendously, but at least it would be much more realistic.

At least such studies are a good start. Given more realistic conditions or more detailed genetic analysis the picture will no doubt get clearer. However, it is obvious even from these results that evolution is more than capable of producing beneficial mutations through random processes. It is also obvious that this will lead to an increase in information after selection acts.

Romans 1:25 who exchanged the truth of God for a lie, and worshiped and served the creature rather than the Creator, who is blessed forever. Amen.

In their use of the deleterious effects of mutations, it seems to me that the ID/Creationist crowd has capitalized on the colloquial image of mutations. The images that come to the public’s mind are things like ugly cancerous blobs, the typical science fiction movie monster, and other disgusting slimy things that are considered “bad”.

The use of the term “mutation” in biological systems is implicitly a more technical use that differs greatly from the image conjured up in the public mind by horror movies.

If their past tactics are any clue, the misuse of this term by the ID/Creationist is deliberate because of its emotional impact (much like the emotional impact of “blind randomness”). It is the kind of use that fires up revulsion in their followers and which can then be used to convince the followers that evolution can’t be right because it is so revolting to think that their god would employ such a device in the creation of the world.

However, if one considers the same idea of a “mutation” in a non-living system that undergoes a sudden shift and then evolves along a different path, there is nothing strange about the idea at all. Just because a system, living or non-living, evolves along a different path after a shift is neither good nor bad, it just happens. If the path leads to survival in the current environment, that’s all that counts. There is no target involved. The system isn’t aiming at some kind of “beauty” in the eye of a human beholder.

It is the perceived “ugliness” that is being exploited by the ID/Creationist leaders. It works even better in a crowd that is somewhat narcissistic and looks in the mirror only to confirm skin-deep appearance rather than for something more substantial.

ID/Creationist leaders know how to exploit ignorance and shallowness.

It is the perceived “ugliness” that is being exploited by the ID/Creationist leaders.

What is the rate of beneficial intelligent designs?

With an answer to that question, then we can compare the two rates, to see which is a better explanation.

("The Edge of Evolution" made me think of one comparison: The effectiveness of human attempts to combat malaria, as compared to the results of human evolution. "The Edge of Evolution" seems to indicate that intelligent (of the human sort) design is less effective.)

WIthout an answer to the question of the rate of beneficial intelligent designs, I don't see how it is possible to make a judgment.

They claim that the sun goes around the earth (26% of them anyway),...

— raven

PvM:

Why must we continue tolerate these idiots here? They don’t want to discuss anything, let alone science, in a civilized fashion, they’re only out to ridicule and condemn those people who are fortunate enough to not share their smothering stupidity.

Do you have any idea how ironic your statement sounds?

raven Wrote: They claim that the sun goes around the earth (26% of them anyway),… I have no reason to disagree, but am curious if you have a reference to that.

Then how do you suggest we communicate with these idiots? They are not interested in actual communication, and are especially not interested in learning anything.

— Stanton

djlactin: I'm not sure the two results can be compared/contrasted that simply: the units seem different. What is the conversion factor between "per cell and generation" (cell^-1 generation^-1?); to "per genome per generation"? In the surface: Since we're talking about asexual reproduction, each genome consists of a large number of cells. Or do the authors assume that each cell has an independent genome? I don't have access to the papers... do the authors try to reconcile the two measures?

As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene.

Calling ID proponents names is not going to make for a very good counter argument.

— PvM

The source is the Gallup GSS, general social survey poll for either 2004 or 2006

— raven

I have been a lurker for some time. And very much a layman. I feel like I am entering the lion's den! Here goes...

To me 'beneficial' or 'degradatory' are only labels to mutations that are determined by us while thinking about some context. If the context changes, e.g. the environment changes, in some way a mutation may be beneficial for that change but in a different context the mutation may be degradatory. For some cases the mutation clearly just kills the organism but these cases are not very interesting and clearly not beneficial!

I think I understand how the experiment described does address this question. I have a slightly different question that, I think, is more directly relevant to the speciation conundrum: Can we see major changes through the different mechanism that we now know exist? (See the list of 43 mechanisms described by another citation I can not now find!) We see lots of evidence in the DNA but the ID folks as well as just layfolk are often demanding more 'direct' proof. I would like some as well

Have there been any simulations, some kind of artificial life programs, than show speciation? For species I am happy to use a common (layman) definition of species that says that individuals of two different species can not breed. This would mean a simulation that has a kind of breeding between organisms that can be observed in such a way that if a species forms, it can be noted. I would assume that having variable environments within the simulation would be useful to provide niches to encourage species to form.

A reference to either such work or a better place to ask this question would be appreciated.

Thanks to all and keep up the great work.

Jeff

Don;t worry the next posting will address the evolution of complex systems in living organisms, not just evolutionary models.

Of course, a well described example is gene duplication which has been studied in quite some detail. Soon we will see ID proponents argue that gene duplication was intelligently designed :-)

What we have seen is how when presented with evidences of evolution of beneficial mutations, ID creationists are quick to claim.... but but but there is also much evidence of stasis. Invariably they seem to quote mine irrelevant papers even though the fact of stasis is well documented at the phenotype level. However, at a genetic level, despite appearance of stasis at the phenotype level, variation can be rampant. Which is the relevance of these findings that most beneficial mutations tend to be of small strength. Of course, this allows them to occur and spread more effectively than mutations which have a large impact and thus come to fixation causing much of the variation in the genome to disappear. That's why the malaria parasite is such a poor example since it involves two hosts, sexual and asexual reproduction and a parasitic relationship.

Malaria parasite - Mosquito - Human

To use this as a common example of evolution is just grasping at straws. Of course, despite these complexities, the evidence for evolution is quite strong, sadly it involves the evolution of resistance to common malaria medication. Resistance is much simpler here because it is a simple selective process for the malaria, although humans are trying to come up with an ever changing environment by using cocktails of medication, and varying medication with other direct methods to kill the musquitos.
Only through a multi faceted approach can one expect to eradicate malaria. Spraying DDT alone in large quantities merely hastens the immunity to DDT.

There are some excellent webpages on malaria and the reproductive cycles, very useful. So ask yourself, has ID attempted to model these interactions in any relevant form to understand evolutionary pressures?

Of course not, ID is not in the business of studying science, just on quote mining data.

Luskin is now arguing that the 10^-20 number is not a guess but rather a well established data point. After all a researcher mentioned it, in passing, and explained in another paper that it was just a guess. Matzke showed how Behe did not do his homework here.

Southeast Asian J Trop Med Public Health. 1999 Sep;30(3):460-9.Links Insecticide cross-resistance spectra and underlying resistance mechanisms of Sri Lankan anopheline vectors of malaria.Karunaratne SH. Department of Zoology, University of Peradeniya, Sri Lanka. Present status of insecticide resistance was investigated in two major vectors of malaria; An. culicifacies and An. subpictus, collected from a high malaria transmission area in Sri Lanka during 1996/1998. Adult and larval bioassays were carried out to obtain log-probit mortality lines for malathion, propoxur, permethrin and chlorpyrifos. Respective LD50 values were 4.45%, 0.002%, 0.16% and 0.001% for An. culicifacies and 0.66%, 0.004%, 0.004% and 0.04% for An. subpictus. Adults were also tested for WHO standard discriminating dosages of malathion, propoxur, permethrin, DDT, cypermethrin, deltamethlin and lambda cyhalothrin. Both populations were highly resistant to DDT. An. culicifacies was more resistant to malathion and An. subpictus was more resistant to chlorpyrifos. About 25% of both populations were resistant to permethrin. An. culicifacies was susceptible to propoxur, deltamethrin and lambda cyhalothrin and An. subpictus to cypermethrin and lambda cyhalothrin. Adult mosquitos were individually tested for their insecticide detoxifying enzyme activities and altered target-site, acetylcholinesterase. High general esterase activity indicated the presence of amplified esterase genes in both populations. Native gel electrophoresis resolved one elevated esterase isoenzyme, with high affinity to organophosphates, from each species. Malathion carboxylesterase mechanism was present in both populations. Higher glutathione-S-transferase activity was marked in An. subpictus. Synergistic studies showed the possible involvement of monooxygenases in resistance in both species. Acetylcholinesterase activity of approximately 80% of both populations was not inhibited by a standard dosage of propoxur. Low resistance to carbamates shows that the impact of agricultural pesticides is not significant in the development of resistance especially in An. culicifaies. Pyrethroids, other than permethrin, can be successfully used in vector control programs. Carbamates will be an alternative.

We see lots of evidence in the DNA but the ID folks as well as just layfolk are often demanding more ‘direct’ proof. I would like some as well.

— Jeff McKenna

Who doesn’t want more direct “proof” (I assume you mean “evidence”)? The difference is that IDers have no interest in demanding any evidence to support their position. In fact, other than “some designer did something at some time,” we don’t even know what the ID position is to begin with. Unfortunately, when it comes to scientific solutions vs. alternatives in general most people have have already been sold on such a double standard. And IDers exploit that to the max.

PvM: First of all, it is not all about them as you yourself pointed out. There are lurkers interested in ID who can benefit from a polite though strong rebuttal. Calling ID proponents names is not going to make for a very good counter argument. Secondly, the more committed ID proponents need time and be told forcefully but again without necessarily using ad hominem terms that they have been misled. Remember that many ID proponents are just repeating what they have been told and have accepted based on authority. We need to show that not only the authority is flawed but that the real science shows a very different picture. This is a long process as there are many vested emotions involved.

Responding here to the original blog entry:

I think it is interesting to see new data regarding mutation rates and the relative occurence of beneficial as opposed to deleterious or neutral mutations. Despite what the creo dupes may say, this directly contradicts much of the creationist literature, i.e. claims such as Behe's (that beneficial mutations are few and far between, while deleterious ones are the norm).

Jeff McKenna asked,

"Have there been any simulations, some kind of artificial life programs, than show speciation? For species I am happy to use a common (layman) definition of species that says that individuals of two different species can not breed. This would mean a simulation that has a kind of breeding between organisms that can be observed in such a way that if a species forms, it can be noted."

I'm pretty sure, Jeff, that fruit flies have been bred in the laboratory until two strains from the same original population became so different they were unable to interbreed. I think Theodosius Dobzhansky was involved in some of those experiments. (I'm doing this off the top of my head, so I hope some professional scientists can jump in here with references.) The IDers have some excuse why this wasn't speciation, but it fits your criteria exactly.

In nature, it's hard to see speciation because it takes so long with large organisms. But one phenomenon scientists consider proof of evolution is "ring" species. This is where a species' range happens to form a ring. Black-backed gulls and herring gulls, for instance, are found in the north temperate zones all the way around the North pole. If you go to, say, Alaska, you'll find one species of gull that's intermediate between black-backed and herring gulls, and is a standard species, all the male gulls able to breed with any of the female gulls. If you travel east across Canada, you'll still find just one species, looking (I think) more and more like herring gulls. Travel across Russia, and it's still just one species, but looking more and more like black-backed gulls. Until finally you get to England and-- the black-backed gulls can't breed with the herring gulls! So the gulls form one species in Alaska, and in every step of the way across both Canada and Russia-- but two species where the two ends of their ranges overlap.

There are a few other ring species. There's a California salamander that lives in the mountainous areas ringing the San Joaquin Valley, and IIRC, a freshwater fish that rings the Appalachian Mountains.

Again, IDers have some excuse why ring species aren't proof of evolution. But descent with modification, as Darwin originally called evolution, is the best explanation for ring species that anyone has come up with to date.

Hope these examples are helpful to you.

I had this idea of reframing the word mutant by having a teacher ask: "You and your brother both came from your parents, but you look different, so which one of you is the 'mutant'?"

Then I remembered what I thought of my brother when I was in school.

hoary puccoon said:

Jeff McKenna asked, "Have there been any simulations, some kind of artificial life programs, than show speciation? For species I am happy to use a common (layman) definition of species that says that individuals of two different species can not breed. This would mean a simulation that has a kind of breeding between organisms that can be observed in such a way that if a species forms, it can be noted."

I'm pretty sure, Jeff, that fruit flies have been bred in the laboratory until two strains from the same original population became so different they were unable to interbreed. I think Theodosius Dobzhansky was involved in some of those experiments. (I'm doing this off the top of my head, so I hope some professional scientists can jump in here with references.) The IDers have some excuse why this wasn't speciation, but it fits your criteria exactly. In nature, it's hard to see speciation because it takes so long with large organisms. But one phenomenon scientists consider proof of evolution is "ring" species. This is where a species' range happens to form a ring. Black-backed gulls and herring gulls, for instance, are found in the north temperate zones all the way around the North pole. If you go to, say, Alaska, you'll find one species of gull that's intermediate between black-backed and herring gulls, and is a standard species, all the male gulls able to breed with any of the female gulls. If you travel east across Canada, you'll still find just one species, looking (I think) more and more like herring gulls. Travel across Russia, and it's still just one species, but looking more and more like black-backed gulls. Until finally you get to England and-- the black-backed gulls can't breed with the herring gulls! So the gulls form one species in Alaska, and in every step of the way across both Canada and Russia-- but two species where the two ends of their ranges overlap. There are a few other ring species. There's a California salamander that lives in the mountainous areas ringing the San Joaquin Valley, and IIRC, a freshwater fish that rings the Appalachian Mountains. Again, IDers have some excuse why ring species aren't proof of evolution. But descent with modification, as Darwin originally called evolution, is the best explanation for ring species that anyone has come up with to date. Hope these examples are helpful to you.

bornagain77:A little more evidence for stasis you may find interesting.. There are many ancient bacterium fossils recovered from salt crystals and amber crystals that have been compared to their living descendents of today. Some bacterium fossils, in salt crystals, dating back as far as 250 million years have had their DNA recovered, sequenced and compared to their offspring of today (Vreeland RH, 2000 Nature). Scientists accomplished this using a technique called polymerase chain reaction (PCR). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost exact DNA sequence. “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; (The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes) http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637

At the Fatty acid level the differences are approaching but have not reached separate species status.

Yes Bornagain confused the 99% similarity in a single gene with the whole genome being virtually similar, as later research showed, there was at most a 70% overlap.

Thanks for posting these updates, resolving these minor myths. I can understand why Bornagain would use these examples without double checking the sources, they are quote mined on various well known creationist sites.

Will these sites correct their errors? Unlikely.

GuyeFaux: What does "separate species status" mean here:

At the Fatty acid level the differences are approaching but have not reached separate species status.

hope this helps

— Albatrossity

So “separate species status” is “just” a statistical measure. It would be good to know what the measure is and what the threshold is.

GuyeFaux:

hope this helps

— Albatrossity

It does. So "separate species status" is "just" a statistical measure. It would be good to know what the measure is and what the threshold is. I'll look into what these are.

These data indicate that at the fatty acid level, the four Permian strains represent two different biotypes. Compared to more modern species, the data clearly show that these are different microbes. The data of fig. 1 show that the Permian microbes can probably best be considered as subspecies of V. marismortui

So “separate species status” is “just” a statistical measure. It would be good to know what the measure is and what the threshold is.

Dembski would go the statistical distribution curve, convert the deviation from the mean to a probability, then take negative log to base 2 and show that “macroevolution” is impossible.

Just to re-emphasize (not that it matters to liars) I’m only interested on what “separate species status” means w.r.t. “fatty-acid level differences” since I’ve never heard of species being delineated in this way.

I hope you didn’t think my comment was directed at you, GuyeFaux.

So I wonder which type of species is preferred.

GuyeFaux wrote:

"If I were an ID/Creationist, I wonder if I would be happier with lots of species with small variation, or fewer species with lots of variation."

It doesn't really matter, since we have many examples of both patterns. And you are right, in both cases the strength of the other argument diminishes. Evolution is entirely capable of producing both patterns and many more.

I suspect that creationists would be most happy with very few species and little or no variation within species and lots of divergence between species. Indeed this was probably what most people assumed before modern genetics and taxonomy came along. Of course, we now know that this is certainly not true generally, although I would not be surprised if most people still believed it.

Indeed, many are now advocating a species definition based on genetic discontinuity. This is similar to the fatty acid idea, but more general. It also gets around the problem of asexual reproduction inherent in the biological species definition. The problem with this approach lies in determining how much discontinuity is required in order for two things to be considered different species. The answer is probably not going to be a simple one.

Indeed, many are now advocating a species definition based on genetic discontinuity. This is similar to the fatty acid idea, but more general. It also gets around the problem of asexual reproduction inherent in the biological species definition. The problem with this approach lies in determining how much discontinuity is required in order for two things to be considered different species. The answer is probably not going to be a simple one.

If you start with a simpler idea with non-living matter first, you get some idea of the complexity of how to define a “species”.

Consider things like dendritic growth of various kinds (mineral growth, the branching out of avalanches, the growth of separate icicles from water dripping off the edge of a roof, water percolating through granular material, etc.) Where to the separate branches become clearly identifiable as separate branches as the system progresses? How would one label these during the early stages?

Now think of the entire panoply of life that exists and has existed on this planet. It appears very much like “dendritic growth” if you consider the entire sweep of it. It is energy driven, and it branches into many paths, any one of which is allowed and determined by the physical conditions in the environment at the moment.

Where does one start labeling separate species? After the separate branches become distinct, there is justification for giving the branches separate names. But at the early stages of branching, we have no solid statistical measure of which way things will go, so any small “deviation” can become the focus of attention and a label for a new species.

Thus, it seems, labels early in the stages of branching are arbitrary and statistically inconclusive.

Marginally on topic--

There seem to be a lot of cases where scientists have been able to breed fertile offspring from multicelled, sexually reproducing species that are closely related but virtually never hybridize in the wild. (Coydogs, i.e., coyote-dog crosses, are an example.) This often involves tricking the females, since the sexual signals of the two species are different.

That indicates to me that the big drive behind speciation is natural selection, more than mutation. Two populations of the same species specialize in two environmental niches. Offspring which aren't specialized for either niche are disproportionately eliminated. Mutations that change the courtship signals so that they diverge are favored, so that there are fewer intermediate offspring. The eventual divergence of the two groups until they cannot produce fertile offspring is just the result of accumulated mutations, not the driving force behind the speciation.

In the case of coydogs, the males follow the dog pattern of not helping to raise the pups, as male coyotes would. And the females give birth at one season of the year, like coyotes-- but the birthing season is shifted 3 months, so the pups arrive in the dead of winter instead of the start of spring. Add to that the fact that coyotes consider dogs something good to eat, and it makes sense that two groups of animals which are interfertile and have lived together in the American Southwest for at least twelve thousand years, have never hybridized into one population.

Henry wrote:

"Yeah, in the case of asexual species, wouldn’t that make “species” just another rank like genus, family, etc., and just as arbitrary?"

Exactly. If you can't use the biological definition of a species with asexuals, then the distinction is already arbitrary. At least using discontinuity the distinction is quantifiable, if still somewhat arbitrary.

Mike is also correct in that the process of speciation can be very difficult to predict in the early stages. Thus, a certain amount of divergence might be required in order even recognize when a new species has arisen.

Hoary also makes a good point, in that reproductive isolation can be produced by many mechanisms that do not involve genetic divergence, at least initially. So once again, the discontinuity criteria may not be useful in the early stages of speciation.

I really hate to agree with everybody, but you all make such good points. Perhaps we can find someone else to argue with later.

I really hate to agree with everybody, but you all make such good points. Perhaps we can find someone else to argue with later.

Any guesses as to how these results would impact human evolution? (i.e., can we use the relative genome sizes, etc, to estimate the beneficial mutation rate in humans or pre-humans?)

The closest I've seen to an attempt to do this is:

http://christianforums.com/showpost.php?p=15972001&postcount=31

(NB: was posted in 2005, when the 2007 report was unavailable)
But I'm sure there are better estimates out there...