Future Risk Assessment in the Genome

This is also yet another level of unexpected specified complexity to be explained. It is clear that random mutation is not as random as we thought.

Why is this so? I do not think, in the standard model of evolution, the important genes need to be marked as important. Would it not be OK for natural selection to do the work of preserving the important genes? Even if they do need to be marked, who is there to mark them? No designer allowed, where does the marking come from?

It’s surprising that this is not presented as a challenge to Darwinism in the article. Somebody has to do the marking; somebody has to say to this gene, “you need some bodacious TATAs.”

You need this unprecedented level of protection against mutation in deep time.
That is untill you realize that “deep time” is another one of the stories that was necessary for the Darwinists story to have any plausibility.

DaveScot in regards to this,

When the cost of error is high, an investor’s willingness to chance the risk is low, but if the cost of a mistake is negligible, even if the chance of making one is high, the possibility of gain may make the risk worthwhile. Evolution, it seems, discovered this principle millions of years before Wall Street.

Seems to me there is a huge amount of “insider trading” going on in the Genome in this scenario, as far as future information is concerned that would be of benefit to future life forms.

And that’s illegal in science as well as on Wall Street!

(Slightly) off topic.

Speaking about Specified Complexity, I just saw this remarkable documentary: “Rivers and Tides” (links at bottom). It is about artist Andy Goldsworthy who creates art works in nature using natural materials. For example, he might create a work in the forest using leaves. For this reason, his works are often (but not always) transient.

What got my brain it a twist is that you could be walking in the forest, see a “thing” made out of the same things that the rest of the forest was made out of, but be able to immediately recognize it as “art”: it had specified complexity whereas the rest of the forest does not (or at least has a different kind of specified complexity).

It is reminiscent of the Mount Rushmore example, But that example only makes sense if you know what a human face looks like. That requirement is removed when viewing Andy Goldsworthy’s art. You would say that it is both in nature and of nature. But it is not natural. It uses a more abstract level of specificity than, say, Mount Rushmore.

I would heartily invite anyone who is thinking deeply about specified complexity to view this film. I think it will give you a whole new perspective.

Here are some links:
http://www.imdb.com/title/tt0307385/
http://www.amazon.com/Andy-Gol.....B0002JL9N6
http://www.netflix.com/Movie/R.....s/60027273

DaveScot off topic sort of:

In regards to verifying Genetic Entropy, I found this research interesting:

http://www.terradaily.com/repo.....s_999.html

of special note:

“That led me into thinking there’s something weird about these very primitive Cambrian trilobites that you don’t see in other (more recent) ones,” he said.

The only way to verify his hunch was to conduct an analysis that combined the data compiled in previously published reports. “It’s too much for one person to look at a thousand trilobite species,” Webster said.

So for his Science study, Webster combed through 68 previously published studies of trilobites, searching for descriptions of evolving characteristics that could be incorporated into his analysis. After eliminating studies that were inappropriate for inclusion, 49 still remained.

He focused on actively evolving characteristics. The trilobite head alone, for example, displays many such characteristics. These include differences in ornamentation, number and placement of spines, and the shape of head segments. His findings: Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so.

“There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.”

Paleontologists have proposed two ideas to account for why variation within species declined through time. One is ecological. In the very early Cambrian seas, fewer organisms existed than today, which meant that they faced less competition for food. “You didn’t really have to be tightly specialized to make a living in the Cambrian,” Webster said.

But as evolution gave rise to more varieties of organisms, ecological communities became more diverse. “You had to be very fine-tuned to your particular niche to make a living and to beat out competitors for a limited resource.”

The genomic hypothesis offers a second explanation for the decline of within-species variation over time. According to this idea, internal processes in the organism were the key factors. Various developmental processes interact with one another to control the growth and formation of body parts as any organism progresses from egg to .

“It’s been suggested that early on in evolutionary history, in the Cambrian Period, the degree to which these different developmental processes interacted with each other within the organism was a lot less,” Webster said. “As a result, the constraints on what the final organism looked like were relatively low.”

Well Dave, what do you think?

I bet this pattern will hold across the board for all species that have exceeding long spans in the fossil record, and I also think it is directly attributable to loss of genetic diversity and clearly conforming to the principle of Genetic Entropy.

It is the most reasonable explanation. When I think about no matter how they dress it up it is in direct opposition to what evolutionary theory would predict…i.e. We see a culling of variety, not a searching for new pathways to take advantage of!

Hi, Dave:
As I pointed out on my own blog, this is relatively easily explained as a consequence of stabilizing selection. During a transition from one stable phenotype to another, the “engines of variation” (listed here) produce a population of individuals with a range of modified phenotypes, some of which survive and reproduce more often than others. The preservation and resulting increase in frequency of such modified individuals over time constitutes directional selection.

However, once an evolving population reaches a state in which the mean phenotypic type has the highest relative fitness, then stabilizing selection replaces directional selection and the population stops changing significantly. This stasis then persists as long as the ecological niche of the stable population doesn’t change significantly.

Under such conditions, any mechanism that might increase the stability of the evolved phenotype in a stable ecological niche would have a higher relative fitness than one that was continually producing new variations at a rate equivalent to that during the evolutionary transition to the new stable state. Therefore, modifications of the promoters to the genes undergoing selection would be selected for in organisms that have undergone one or more periods of evolutionary stasis (as defined by Eldredge and Gould).

Indeed, this finding strongly suggests that the “engines of variation” that I listed in my own blog have a throttle: that is, the amount of variation that can be produced in any given gene is not fixed (i.e. it is not really “random”), but rather can increase or decrease as the result of selection. This possibility presents the very exciting possibility that we will be able to explain the apparent bursts of variation that accompany major ecological changes, such as the major adaptive radiations that have accompanied the five major mass extinctions on Earth. Far from being a problem for evolutionary biology, this finding is in fact a potentially major advance in our understanding of what G. G. Simpson called “tempo and mode” in evolution.

I note from the rest of the article that Prof. Barkai is studying evolutionary events (such as genome doubling) by comparisons between distantly related species. This assumes common descent (…apply that approach to Plasmoidum vivax and Plasmodium falciparum - and one gets a few dark grey swans).

The other key point is causality - there’s an association between TATA binding sites in promoters and conservation of the gene, but does this just reflect the physiological role of TATA binding sites - e.g. not being infront of house-keeping genes and therefore not subject to purifying selection i.e. the presense of TATA is an epiphenomenon, rather than a cue for non-conservation.

Thirdly this finding is associated with conservation (or not) of expressed genes - rather than a mechanism to conserve unused front-loaded information.

Allen_MacNeill,

Please list your source for CSI (complex specified information) generation i.e. What genetic mutational study lays the foundational framework for your latter assertions? i.e. Why should your your hypothesis be considered viable as far as generating the required information (CSI) it absolutely needs exactly when it needs to when all mutational studies, I know of, rule out your scenario from first principles even in the most favorable of circumstances?

“You don’t seem to get it even though people keeping correcting you…universal common descent does not add even one dark speck to “All complex biological systems are generated by intelligent agents.””

Feel free to pop back to the P.falciparum thread to discuss it. I’m just pointing out that comparison between closely related species of Plasmodium suggests hundreds of genes have appeared since divergence, with complex new functions associated with the genes. But this information (and the TATA stuff) is only valid if common descent is accepted.

In case some of your readers might be interested in more on this topic, here is a link to a discussion of it on my blog. In that blogpost, I ask the following question:

• Is the rate of generation of genetic and phenotypic variation a constant?

I then point out that if the answer is “no,” then a new question immediately follows:

• Is the increased rate of generation of variations correlated with any identifiable factor in either the genetics/development or the environment of organisms in which such variable rates of variation are observed?

If the answer to this question is “no,” then we may safely assume that the underlying “engines of variation” are probably random, insofar as we can observe phenotypes changing randomly over time.

However, if the answer is “yes” (and the research report that is the sutbject of this blogpost strongly suggests that it is), then this suggests another question:

• Via what mechanism(s) is the increased rate of variation generated, and are the “triggers” for such increased variation endogenous, exogenous, or some combination of the two?

According to the article, the answer is (not surprisingly) a combination of the two. That is, the TATA box provides a switch that responds to a signal from the environment;

• If the environment is becoming more variable, the switch throttles up the rate of production of variation

• If the environment is becoming more stable, the switch throttles down the rate of production of variation

If evolutionary theory is a reasonable explanation for the origin of biological diversity, then the “engines of variation” are prodigious, as they have been able over time to modify something as simple as a mycoplasm into an oak tree or a blue whale. Some supporters of “intelligent design” (ID) would dispute this statement, of course, claiming (without any empirical evidence) that “you can’t get here from there.” However, as Michael Behe, MikeGene, and other ID supporters have clearly asserted, we have gotten here from there; the real question is “how?” There are logically at least two possibilities:

• The processes by which the “engines of variation” have produced the necessary variation have operated endogenously by means of a prodigious (and undirected) “random variation generator,” the products of which have been sorted over time by natural selection (i.e. the Darwinian hypothesis)

or

• The processed by which the “engines of variation” have produced the necessary variation have operated endogenously by means of a series of equally prodigious “non-random variation generators,” the products of which have been sorted over time by natural selection (i.e. the ID hypothesis).

Notice that in both cases, natural selection is what finally determines what exists and what doesn’t. The intelligent designer of ID theory, in other words, works virtually exclusively through modification of variation, allowing natural selection to preserve those variations that it has intelligently designed.

Noticing that the only difference between these two possibilities is the amount of variation and its source also immediately suggests a way of testing the two hypotheses:

• Do the currently identified mechanisms of genetic and phenotypic variation produce enough variation to get from there to here or not?

If the answer is “yes,” then the ID hypothesis is unnecessary, and therefore irrelevent to science. If the answer is “no”, then ID may have something very significant to contribute to science.

However, the only way to answer this question is to do the relevant empirical research, testing falsifiable hypotheses that distinguish clearly between the two. So far this has not been done, especially by IDers. Therefore, it is clearly not yet time for either side to declare that this is a settled question. To declare otherwise is not science but propaganda.
–Allen
*********************************
Allen D. MacNeill, Senior Lecturer
The Biology Learning Skills Center
G-24 Stimson Hall, Cornell University
Ithaca, New York 14853
*********************************
phone: 607-255-3357 (Allen’s office)
email: adm6@cornell.edu
website: http://evolutionlist.blogspot.com/
*********************************
“I had at last got a theory by which to work”
-The Autobiography of Charles Darwin
*********************************

Hi, I’m new here, and I find the information very enlightening. I’ve been confused a bit by one thing that Patrick brings up in #14 above, namely his statement that “…we should continue researching.” While a believer myself, and being a strong adherent to the design inference, I’m troubled by what seems to be a dearth of actual research on the part of ID advocates. Who is the “we” that Patrick refers to?

Allen_MacNeill you stated:

However, the only way to answer this question is to do the relevant empirical research, testing falsifiable hypotheses that distinguish clearly between the two. So far this has not been done, especially by IDers.

I take issue with that statement.

Since Patrick already pointed to Dr. Behe’s work, in which malaria was subjected to extreme pressure to evolve complexity and failed to generate even one novel protein/protein binding site.

I will refer you to my post on #7, it is one of many studies verifying the principle of Genetic Entropy (the marriage of the second law with conservation of information) (The exact opposite of the evolutionary theory). This study is unique in that it clearly demonstrates loss of variability over approximately 250 million years for trilobites:
I maintain that over 250 million years severe environmental pressure would have been introduced at some time for the trilobites to evolve more complexity not less!
Thus your assertions are found wanting in only this first study I’ve collected for long time span analysis of a species!

http://www.terradaily.com/repo.....s_999.html

Of special note:

So for his Science study, Webster combed through 68 previously published studies of trilobites, searching for descriptions of evolving characteristics that could be incorporated into his analysis. After eliminating studies that were inappropriate for inclusion, 49 still remained.

He focused on actively evolving characteristics. The trilobite head alone, for example, displays many such characteristics. These include differences in ornamentation, number and placement of spines, and the shape of head segments. His findings: Overall, approximately 35 percent of the 982 trilobite species exhibited some variation in some aspect of their appearance that was evolving. But more than 70 percent of early and middle Cambrian species exhibited variation, while only 13 percent of later trilobite species did so.

“There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.”

Allen_MacNeill, what do you want to bet that every long term analysis of a species I can get my hands on will fall into this loss of variability category, thus conforming to Genetic Entropy,,,,Thus, I am making a clear prediction that can clearly be falsified,,,Indeed if variability is found to increase over long periods of time in the fossil record then Genetic Entropy will be tentatively falsified…That is a lot more than I can say for evolution for, from what I’ve seen, evolution can never be falsified!

Adam Rutherford, (the “impartial” reviewer of the NOVA PBS production “Judgement Day” in Nature http://www.nature.com/nature/j.....0170a.html ), can perhaps help enlighten us on why not much overt ID research gets done in our universities.

“Guillermo Gonzalez has been denied a physics post by his university. Quite right: you cannot believe in ID and call yourself a scientist. So farewell, I hope, to the scientific career of Guillermo Gonzalez. … I know that, were I in a position to offer Guillermo Gonzalez tenure, I would deny it for the precise reason that his, yes, religious views about purpose in the universe explicitly mean he is a crap scientist, regardless of his ability to generate valid data. … As a vocal supporter of the demonstrably unscientific guff that is intelligent design, Gonzalez displays ignorance of the scientific process, and appears to wilfully [sic] defy it. And for that reason, he neither deserves the use of the facilities of a university to conduct scientific research, nor the privilege of teaching the next generation of scientists.”

http://commentisfree.guardian......esign.html

In response to comment #16 by bornagain77:

As Niles Eldredge and Stephen Jay Gould pointed out almost three decades ago, the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time. This is clearly the case among east African cichlid fish, such as those in Lake Malawi and Lake Victoria. As numerous studies have pointed out, Lake Victoria is only a little over 12,000 years old, while Lake Malawi is approximately 1.5 million years old. Lake Victoria has (or had, until the introduction of the Nile perch) over 600 species of cichlids, while Lake Malawi has many, many fewer (the exact numbers are not known, due to rapid species turnover and the difficulty of sampling fish species in these lakes). In other words, the older the lake, the lower the species diversity.

This general pattern is also observable among the arthropod phyla in the “Cambrian explosion”, the vertebrate tetrapod taxa following the Permian-Triassic mass extinction, and the mammalian phyla following the Cretaceous-Teritary mass extinction. This is precisely what macroevolutionary theory predicts: adaptive radiation, followed by species “pruning”, caused mostly by increasing niche specialization and the squeezing out of marginally adaptive taxa.

Over deep evolutionary time, however, species diversity has shown a steady increase: there are more species of animals alive today than at any time in the preceding 600 million years. That is, although species diversity declines within taxa, the overall number of higher taxa increases over time. This is because macroevolution includes a kind of “rachet”: mass extinctions rarely if even eliminate an entire set of higher taxa. Even the Permian-Triassic mass extinction didn’t kill all of the multicellular organisms on Earth (only about 99% of them). And then, as the surviving taxa rapidly diversified into the now-vacant adaptive zones, the new taxa were added to the survivors.

Is this version of macroevolutionary theory non-falsifiable? On the contrary, it could easily be falsified by showing (in the fossil record) that intra-taxonomic diversification increases steadily over deep evolutionary time. This finding would verify the gradual diversification model that Eldredge and Gould called “phlogenetic gradualism” and falsify their alternative hypothesis of “punctuated equilibrium.” However, as more and more evidence has accumulated about the adaptive radiation of various taxa following major extinctions, it is clear that Eldredge and Gould’s model has more empirical evidence supporting it.

Now, just how much empirical evidence has ID going for it? The only published books and papers that I’m aware of (and I’ve read almost all of them, and assigned them as required reading in my evolution/design seminar last summer) are theoretical models and alternative interpretations of already existing evidence, virtually all of it collected and published by evolutionary biologists. Until IDers start doing actual empirical science of their own, their “theories” will remain untested hypotheses, and their ideas will consist virtually entirely of airy speculation.

Want to have your ideas respected by other scientists? Get your hands dirty…

Having participated in tenure decisions on numerous occasions over the past thirty years (including my own, of course), I can honestly say that what makes the difference is – surprise! – money (and to a lesser extent, “collegiality”). If Gonzales had published major papers in the peer-reviewed journals in his field, brought in major grant money to his university, had trained and graduated a growing cadre of graduate students, and had actively participated in the advancement and management of his department, he almost certainly would have been granted tenure. That’s precisely what the public record shows he did not do, and that squares with my experience in academia.

This thread seems to have wandered badly off of its initial track.

I am finding the orignal report to be intriguing. I am trying hard envision the inevitable “just so story” that fits this phenomenon into the RV*+NS hypothesis.

*Where a some of the sources and characteristics of variation are so aptly provided by Dr. MacNeill (see link in #8 above.)

Allen_MacNeill, thanks for the response, now to reiterate a question that is pertinent to this thread:

Please list your source for CSI (complex specified information) generation i.e. What genetic mutational study lays the foundational framework for your latter assertions? i.e. Why should your any part of your hypothesis be considered viable, when you have no mutational study backing you up in the first place that says you can generate CSI in any genome?

Now back to our discussion:

Thanks also for listing the work of Niles Eldredge and Stephen Jay Gould.

Now let’s try to fit the unbiased evidence into the ID/Genetic Entropy framework, and see how much better of a fit we have than the evolutionary scenario does for it.

First you state:

the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time.

Thus the Theistic prediction for ID/Genetic Entropy finds validation in this work you cite.

Now let’s see if I got it right:

A fossil (parent species) suddenly appears in the fossil record, with no solid evidence of transmutation from any other fossil form,,,

“… Every paleontologist knows that most new species, genera, and families, and that nearly all categories above the level of family appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences.” George Gaylord Simpson (evolutionist), The Major Features of Evolution, New York, Columbia University Press, 1953 p. 360.

What can be considered to be a parent species, then, rapidly diversifies while sub-species maintain basic morphological robustness of parent species (Am I correct so far?), Then, stability ensues for a while with no new variability ever being found ever again in the sub-species (correct?), Then over longer periods of time, the fossil diversity of sub-species (and even diversity within specific sub-species fossil types) shrinks until most all lineages of the parent species go into extinction. (Correct?).

This fits perfectly with loss of Genetic Diversity studies (i.e. Genetic Entropy)! And is completely contrary to the evidence evolution absolutely needs to be considered viable!

Evolution given long periods of time is losing diversity! It is not searching every nook and cranny for a new niche to fill!

To drive the nail further in the coffin, preliminary genetic diversity studies are backing up ID? Genetic Entropy!:

“We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.” Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.

Also, In this study for ancient Australian (Mungo Man) DNA we have clear evidence of Genetic Entropy being obeyed!:

http://www.pubmedcentral.nih.g.....rtid=33358

Of special note:
Adcock et al. (7) clearly demonstrate the actual extinction of an ancient mtDNA lineage belonging to an anatomically modern human, because this lineage is not found in living Australians. Although the fossil evidence provides evidence of the continuity of modern humans over the past 60,000 years, the ancient mtDNA clearly does not, providing an excellent example of why the history of any particular locus or DNA sequence does not necessarily represent the history of a population. Adcock et al.’s (7

As well, Here is a Paper that has confirmation of dogs and grey wolves staying within principle of Genetic Entropy.

http://jhered.oxfordjournals.o.....0/1/71.pdf

of special note:
Some sequences found in dogs were identical to those in wolves…
The sequence divergence within (breeds of) dogs was surprisingly large: the mean sequence divergence in dogs 2.06 + or - 0.07% was almost identical to the 2.10 + or - 0.04% (sequence divergence) found within wolves. (notice that sequence divergence is slightly smaller for dogs than for wolves)
Coupled with the diverse morphology of domesticated dogs and known hazards of dog breeding, this evidence strongly indicates “front loaded adaptations” at a loss of information from parent species. Thus, this is genetic confirmation of the principle of Genetic Entropy for dogs from wolves!

This overall pattern of evidence (morphology and genetic diversity) conforms strongly to the evidence supporting the principle of Genetic Entropy found for humans.

These following genetic studies of sheep are interesting:

Single male and female sheep maintain genetic diversity.

A mouflon (The parent sheep population) population, bred over dozens of generations from a single male and female pair transplanted to Haute Island from a Parisian zoo, has maintained the genetic diversity of its founding parents.
This finding challenges the widely accepted theory of genetic drift, which states the genetic diversity of an inbred population will decrease over time.

“What is amazing is that s of genetic drift predict the genetic diversity of these animals should have been lost over time, but we’ve found that it has been maintained,” said Dr. David Coltman, an evolutionary geneticist at the University of Alberta.

http://www.sciencedaily.com/re.....103157.htm

This is exactly what the Theistic ID position would have postulated!

Whereas sub-species of sheep always have problems with inbreeding:

Heredity - Diversity and evolution of the Mhc-DRB1 gene in the two …
Low levels of genetic variation were detected in both subspecies, …..

Is the decline of desert bighorn sheep from infectious disease the result of low MHC …
http://www.nature.com/hdy/jour.....1016a.html

Thus conforming to Genetic Entropy.

AS well I wanted to point out that evolution has no foundational princip[les of science in which to build its conjectures! Whereas Genetic Entropy can rest its conjectures on the foundation of the second law of thermodynamics as well as the law of conservation of information!

That is why I will always press you for experimental proof of generation of CSI, for it is impossible for totally material processes to generate CSI in this universe… If you are trying to prove evolution true, You will always be trying to prove something akin to the perpetual motion machine…the simple fact is you will never do it!

Professor MacNeill

While I have no desire to keep the thread off-track, I find it important to put in a corrective.

For, you have unfortunately materially misrepresented Dr Gonzalez’s academic record [he GREATLY exceeded the academic productivity requirements [68 papers (well beyond the 15 stipulated), providing the basis for discovery of two new planets, etc etc], and was in an environment where some 90% of applicants were granted tenure and one in which the man who led a wit^ch-hunt^ing campaign against him (and whose own academic track record has some very dubious “contributions” in it) was rewarded by the university], AND what has come out about why he was denied tenure.

That those who support the denial of tenure cannot frankly face the evident and material facts that have manifestly come out — including right here in this blog — is all too telling.

IDNet.Au and Patrick are right to highlight the NCSE’s indefensible agenda: publish or perish, but if you publish we will persecute the Editor of the Journal [Rick Sternberg] and we will deny tenure [Gonzalez], or drive you out of “our” institutions [Dembski].

And, as a matter of fact, there is in spite of all this, a growing body of relevant empirical research, peer reviewed, peer edited, and more to the point, out there for us to look at and weigh up for our selves. (In a wit^ch-hunt^ing environment, so-called peer review rapidly becomes simply worthless as a criterion of excellence.)

Behe’s Edge of Evolution and the point it shows empirically on the limitations of random variation and natural [as opposed to artificial] selection to create complex novelty, is only the latest and in some ways the most telling.

So, BA’s point that the evidence strongly points to loss of variability and functionality through this process is relevant. So is the point highlighted by Meyer in that paper that cost Rick Sternberg so much to have the courage to publish:

. . . In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes–the very stuff of macroevolution–apparently do not vary. In other words, mutations of the kind that macroevolution doesn’t need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don’t occur.6

That is the challenge to be answered, and so far as I can see, it has not been answered — apart from red herrings leading out to strawmen that have been burned to cloud and poison the atmosphere, and then are backed up by the appeal to the stick.

FOR SHAME!

GEM of TKI

Professor MacNeill you stated:

Is this version of macroevolutionary theory non-falsifiable? On the contrary, it could easily be falsified by showing (in the fossil record) that intra-taxonomic diversification increases steadily over deep evolutionary time. This finding would verify the gradual diversification that Eldredge and Gould called “phlogenetic gradualism” and falsify their alternative hypothesis of “punctuated equilibrium.” However, as more and more evidence has accumulated about the adaptive radiation of various taxa following major extinctions, it is clear that Eldredge and Gould’s has more empirical evidence supporting it.

This is what I mean by unfalsifiable, to restate your very own words:

“This finding would verify the gradual diversification that Eldredge and Gould called “phlogenetic gradualism” and falsify their alternative hypothesis of “punctuated equilibrium.”

You are saying, “If we find variation through deep time for a branch of species (which we categorically don’t) we have a evolutionary theory. Yet if we don’t find a branch of species developing variability then we also have a (punctuated) evolutionary theory.

Thus heads I win tails you lose!

How in the world does this allow evolution to be falsified Professor MacNeill?

My few words to you on the audacity of it all can barely contain my displeasure for how you mistreat the scientific method!

Allen_MacNeill (8): [T]his is relatively easily explained as a consequence of stabilizing selection…. [O]nce an evolving population reaches a state in which the mean phenotypic type has the highest relative fitness, then stabilizing selection replaces directional selection and the population stops changing significantly. This stasis then persists as long as the ecological niche of the stable population doesn’t change significantly. Under such conditions, any mechanism that might increase the stability of the evolved phenotype in a stable ecological niche would have a higher relative fitness than one that was continually producing new variations at a rate equivalent to that during the evolutionary transition to the new stable state. Therefore, modifications of the promoters to the genes undergoing selection would be selected for in organisms that have undergone one or more periods of evolutionary stasis…

According to your hypothesis, the genes without the TATA sequence in their promoters correspond to those for traits that have undergone substantial directional selection and then required stabilization once a stable state was achieved. Presumably, since periods of stasis, followed by periods of change, have occurred repeatedly through time, the longevity of such genes will be fully variable.

However, in the article, it’s implied that the genes without the TATA sequence in their promoters correspond to those for traits that “fulfill some basic, universal function for all life, and changes in their sequences have drastic consequences, involving death or the inability to multiply” and therefore “have been conserved through long stretches of evolution”.

These are not the same thing.

Allen_MacNeill you state:

“then stabilizing selection replaces directional selection”

Yet in your blog you state:

the primary “engine” of evolution has been considered to be natural selection. However, if one takes a closer look at this, it is clear that natural selection is not an “engine,” it is an outcome.

Let’s get this straight, natural selection does not drive evolution,,,when you don’t want it to (first statement),,,yet when you want it to (second statement), natural selection can not only be directional (when you want it to fit the evidence) it can also be stabilizing (when you want it to fit the evidence)

Even if your highly unlikely niche theory were to be true, What in the world is going to tell the Random Variation part of your theory to stop searching variability within a species to fill any random niche that would happen along,,,This is absolutely ludicrous for you to pick and choose what parts of your highly flexible theory you want to operate when you want them to operate.

Your theory is clearly an imaginary conjecture that has no foundation nor place in the scientific method!

correction the statement in post should read:

Let’s get this straight, natural selection does not drive evolution,,,when you don’t want it to (second statement),,,yet when you want it to (first statement), natural selection can not only be directional (when you want it to fit the evidence) it can also be stabilizing (when you want it to fit the evidence)

Allen MacNeill want to be the one to have developed the new “punk eek.” Or rather how punk eek really works and then put himself alongside Gould and Eldredge or maybe a little ahead of them.

I have a little bit of trouble understanding all the gibberish about directional and stabilizing selection. Shouldn’t a variation that is superior to the current stable genome always have a place at the table. After all it will start producing more offspring. And his engines are constantly churning out all these good variations amongst the bad so why should the superior variations be selected against.

I am a little confused. Maybe it would be helpful to dissect MacNeill’s speculations. They seem esoteric but are they really self contradictory.

Jerry,
His theory is unfalsifiable …period.

Whereas the ID/Genetic Entropy are clearly falsifiable and fit the evidence to perfection from the preliminary evidence I have gathered,,,In fact if variability were seen to increase instead of decrease once the parent species has reached maximuim diversification then this would falisify the Genetic Entropy postulation of Sanford.
What does the fossil evidence consistently show,,,.

1. Abrupt Appearance

2. Rapid diversification

3. Long term Stability with no new variability introduced.

4. Loss of specific variability within sub-species types as well as loss of actual number of sub-species to gradual extinction of (most?) all sub species.

This is a perfect conformation to ID/Genetic Entropy hypothesis to its foundational principles(Concervation of Information married to Second Law), Yet evolution cannot explain this to its foundation principles, even though Professor MacNeill obfuscates to the nth degree and pretends it does.

Has anyone found the primary paper yet? It would be good to look at the exact methods - at the moment were going on a description from Prof. Barkai to a Weizmann Institute PR person, to a ScienceDaily journalist.

bFast

“I am trying hard envision the inevitable “just so story” that fits this phenomenon into the RV*+NS hypothesis.”

Coming up - a “just so story” just for you.

It looks like TATA sequences are not placed behind house-keeping genes. This maybe because TATA promoters induce gene expression in a pattern which is ineffective for the genes’ physiological role (e.g. inducible to environmental stimuli rather than constant low level operation).

House keeping genes are critical - hence subject to intense conservation. Genes which are involved in reacting to external stimuli - are subject to adaptation.

TATA is therefore more commonly infront of genes undergoing adaptation. It is a correlation rather than a cause.

Experiment:

Put in or take out TATA promoters infront of genes in yeast, and see whether gene mutation rates change. If the hypothesis (aka just-so-story) is correct then we expect inserted-TATA sequences to be lost, and those that were deleted will probably mutate back. Selection for fitness is driving the position of TATAs, rather than the poition of TATAs driving adaptation.

Cost: ~$30,000

I imagine the DI could stump up the cash for that? and I suspect they could find at least one motivated grad student who could do this type of work.

One of the basic principles of Darwinian evolutionary theory is that there must be sufficient inter-individual variation to allow for phenotypic change over time. Darwin himself pointed this out in the first chapter of the Origin of Species. This concept was further elaborated by Ronald Aylmer Fisher in his book, The Genetical Theory of Natural Selection, now considered to be one of the foundational texts for the neo-Darwinian synthesis of the 1930s and 40s. Fisher’s “Fundamental Theorem of Natural Selection” is still considered to be the basis for all scientific explorations of adaptive evolution, which along with Sewall Wright’s concept of genetic drift, Motoo Kimura’s “Neutral Theory of Molecular Evolution”, and Tomoko Ohta’s “Nearly Neutral Theory of Molecular Evolution” form the basis of virtually all of current microevolutionary theory.

Central to this concept is the observation that all naturally occurring populations exhibit what Fisher called continuous variation. That is, a range of variation in various traits that, when plotted in cartesian coordinates, approximates a normal distribution (i.e. a so-called “bell-shaped curve”). In a trait that exhibits continuous variation, most of the individuals exhibit the trait at a value reasonably close to the mean, with a relatively small number of individuals exhibiting relatively large or relatively small values for that triat.

An example is height in humans, which is often illustrated in introductory biology texts with a group of students (or sometimes military cadets) arranged along a football sideline in order of height. There are a few very short and a few very tall people, but the vast majority form a bulge in the middle of the curve.

Given a population that exhibits continuous variation for a trait, there are three different patterns of natural selection that can result:

Stabilizing selection, in which individuals from both extreme “tails” of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those in the middle bulge of the curve. Under such conditions, the mean value for the trait does not change over time (hence the term “stabilizing selection”). In our example of height, stabilizing selection would be the result if individuals of average height had the most surviving and reproducing offspring (assuming that height is heritable from parents to offspring, of course).

Directional selection, in which individuals from one (but not the other) extreme “tail” of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those in the middle bulge of the curve. Under such conditions, the mean value for the trait changes over time, shifting toward the tail of the curve that includes the surviving individuals (hence the term “directional selection”).

Diversifying selection, in which individuals from the middle of the range (but not either extreme “tail”) of the normal distribution are not preserved over time (i.e. they do not have as many offspring that survive to reproduction), compared with those at the extreme tails of the curve. Under such conditions, the mean value splits and becomes bimodal, with two new mean values increasing in frequency, and the old mean value disappearing. This process would eventually (depending on the intensity of selection) produce two phenotypically different populations where one had previously existed (hence the term “diversifying selection”).

All three types of selection have been observed in nature. By far the most common type is stabilizing selection; that is, most populations appear to be in rough selective equilibrium within their environments, an outcome that was predicted by Eldredge and Gould in their 1972 paper on punctuated equilibrium. Directional selection has also been observed in nature, and is usually correlated with fairly dramatic changes in ecological conditions, such as major ecological disruption correlated with a mass extinction event. Directional selection has also been observed in nature; an example is bimodal divergence in mean beak in African seedcrackers (a finch-like bird), in which seedcrackers with small and large beaks have higher reproductive success than those with average sized beaks.

And so, rather than being a “just-so story” that is finagled to fit the data, these three modes of natural selection, which were first outlined by Theodosious Dobzhansky (one of the founders of the neo-Darwinian evolutionary synthesis and a devout Eastern Orthodox Christian), comprise a comprehensive theory of natural selection that has been repeatedly verified by comparison with data collected in the field by evolutionary biologists and ecologists. Notice, please, that none of these types of selection contradict the others in any way. Indeed, they all depend on the same underlying process that Darwin proposed in 1859: unequal, non-random survival and reproduction among populations of living organisms having continuously variable, heritable traits.

Notice also that the underlying source of new traits is the “engines of variation,” not natural selection, which merely preserves those traits that are carried by those individuals that survive and reproduce. Natural selection, as John Endler and Will Provine have repeatedly pointed out, is not itself a “mechanism,” it is an outcome of the operation of three “mechanisms:”
• variation between individuals in populations
• inheritance of such variations
• reproduction
which together have the effect of producing
• non-random, unequal survival and reproduction
which has the effect of producing
• non-random preservation of particular individuals with particular heritable traits (i.e. adaptations).

So well supported is the foregoing with repeated empirical field and laboratory research that even Michael Behe and William Dembski do not dispute any of it, as evidenced by the fact that they (like most creationists) accept microevolution (i.e. natural selection, sexual selection, and genetic drift) as a strongly supported theory. In my evolution/design seminar last summer, in which Hannah Maxson (founder of the the Cornell IDEA Club) was an invited co-presenter, every participant (i.e. both supporters of evolutionary biology and intelligent design) agreed that there was no rational dispute over the facts or theory of microevolution. Furthermore, Michael Behe (like all but one of our seminar participants) also publicly accepts that macroevolution (defined as the descent with modification of higher taxa from common ancestors) is strongly supported by multiple lines of empirical evidence.

Therefore (and as we concluded last summer), the only real areas of dispute between evolutionary biologists and the major theorists and supporters of intelligent design is the origin of life from non-living material (“abiogenesis”) and the origin of a small number of complex biochemical mechanisms and pathways (including the bacterial flagellum, selected components of the vertebrate immune system, and the mammalian blood clotting cascade, to which Behe has now added the evolution of chloroquine resistance in Plasmodium falciparum). As anyone who has actually read the Origin of Species knows, this leaves absolutely all of Darwin’s original theory untouched and unchallenged, as Darwin never published any theory concerning the origin of life, nor the origin of any biochemical pathway. Furthermore, it leaves virtually all of evolutionary biology untouched, because evolutionary biology is about living organisms (i.e. not the origin of life).

Quod erat disputandem?

*********************************
Allen D. MacNeill, Senior Lecturer
The Biology Learning Skills Center
G-24 Stimson Hall, Cornell University
Ithaca, New York 14853
*********************************
phone: 607-255-3357 (Allen’s office)
email: adm6@cornell.edu
website: http://evolutionlist.blogspot.com/
*********************************
“I had at last got a theory by which to work”
-The Autobiography of Charles Darwin
*********************************

Michael Behe has done no original empirical research into the evolution of chloroquine resistance in Plasmodium falciparum. On the contrary, all he has done is speculate on how this might have come about, using empirical data gathered by other scientists, nearly all of them professionally trained in the dynamics and consequences of evolutionary theory.

Until a practicing scientist actually proposes a testable hypothesis about some aspect of intelligent design, tests that hypothesis with actual field and/or laboratory research which s/he has carried out, has analyzed the results using generally accepted methods of statistical analysis, and published such results, intelligent design is not even a hypothesis (i.e. something than can be empirically tested). It’s just speculation, and therefore doesn’t even begin to approach the threshold of what counts as science.

Dr. MacNeill,

That is a very helpful explanation. I’m not sure what to make of it all, but at least people should stop making the accusation that you don’t know what you’re talking about, that your terms are “gibberish” and your view “esoteric” (jeery), or that you “pick and choose” among selection types (bornagain77). Whatever the merits of your views, these accusations should be laid to rest.

BA77,

I have to ask: what’s with all the commas,,,in your comments?

correction: for “jeery” read “jerry.” I wasn’t playing with his name, promise.

Dr. MacNeill,

In your long post, #31, there is nothing in it relative to selection that is not basic. So there isn’t anything to object to and most of us here will not object. It make common sense.

As an aside, there tends to be an emphasis on traits where there is a distribution and not a on/off distribution. Height, beak size or other physical characteristics often appear in gradations when it is possible that some traits may exist or not exist in an organism. There is nothing here I object to and only wondered how it affected such traits and how many traits are like that.

Natural selection and its different manifestations is really not of interest to me and a lot of ID because it is not the real issue. What really interests me is the source of variation and this seemed to get passed over in your discussion. What confused me is how you seem to blithely integrate the various types of selection with the origin of variation or how much variation can occur or will be allowed to occur.

However, I do object to your brief discussion of macro evolution and whether it is controversial or not. It seems to imply that ID is not interested in things other than OOL issues which is not true.

Macro evolution covers a lot of ground and I am not sure there is good evidence to support all of what is called macro evolution. For example, I would not call most IC systems macro evolution since a lot of it is pre Cambriian or only showed up in the Cambrian. I tend to refer to macro evolution as that which occurred after the Cambrian.

After the Cambrian there is a lot of macro evolution which is purely speculation on how it occurred. Most of the debate in the popular press is how did one species arise from another species when there are substantial functional differences between them. This is the major league of macro evolution. How did insects, birds and bats get wings to fly, how did land creatures develop oxygen breathing systems or how did man get such a big brain and why such a long time for children to develop and where did consciousness come from. How did 4 chamber hearts and warm vs. cold blooded arise. How did birds develop their unique oxygen transport system. There is a lot more but this gets to the issue. There is lots of speculation but no evidence, only as series of “just so” stories. An occasional fossil is brought up to show the progression ignoring the fact that there had to be tens of thousands of other steps for these progressions of which only a handful have been found.

There is another part of this discussion which I call macro-evolution light or the minors. This is how did a lot of the orders and families develop? For example, within Carnivora how did all the families arise? ID seldom cares about this area but evolutionary biology does. I don’t think ID would care much if someone showed how all the family canidae or felidae arose by gradualistic approaches but yet the evolutionary biologists would claim that would be a major verification of their theory.

So I am not sure Behe or Dembski would buy your assessment of macro evolution and you conflate the macro evolution light with all macro evolution and in no way touch the systems that must have been present at origin of the phyla during the Cambrian.

getawitness,

I greatly appreciate Dr. MacNeill’s knowledge and read his post here eagerly and only lament they are too infrequent. He is a fount of information and is certainly aware of what is current in evolutionary biology as much as anyone in the country.

That does not mean I agree with all he says. But as he answers our questions, we learn the edge of evolution in a different way than Michael Behe has outlined. I have not found anything he has said that undermines ID. He may disagree but as of yet I have not seen it.

I just wish he would come here more often because he is so well regarded in his field.