TheologyWeb Campus - Natural Science 301 http://www.theologyweb.com/campus/ Study charts, really long words and throw pens at each other. Creation, Evolution, Anthropology, age of the earth stuff and Biology held here. en Wed, 19 Jun 2013 23:20:52 GMT vBulletin 5 http://www.theologyweb.com/campus/images/misc/rss.png TheologyWeb Campus - Natural Science 301 http://www.theologyweb.com/campus/ <![CDATA[Dobzhansky's predictions flop ...]]> http://www.theologyweb.com/campus/showthread.php?156347-Dobzhansky-s-predictions-flop&goto=newpost Mon, 17 Jun 2013 13:44:29 GMT This is a superb article centered around Theodosius Dobzhansky's infamous
article "Nothing in Biology Makes Sense Except in the Light of Evolution."

That title has since been endlessly parroted by the Evo-Faithful and is
considered by the Evo-Flock to be a "fact, Fact, FACT of modern biology".

Well, the article makes mincemeat out of Dobzhansky's statement and
predictions that Dobzhansky advanced based on that religious belief.

The ending of this article is as beautiful as it is conclusive (my highlights) :

"Just as the Marxists spent decades inventing economic interpretations
of everything, so too evolutionists endeavor to create Darwinian
explanations for everything (Prager, 2012) ... Ignoring Darwinian
narratives of alleged deep time and considering instead actual
biological discoveries, such as those that earn Nobel Prizes, evolution
is surprisingly irrelevant according to dozens of the world’s leading
scientists, as assessed by a member of the prestigious National Academy
of Sciences.

Philip Skell reports that he “asked more than 70 eminent researchers if they
would have done their work differently if they had thought Darwin’s theory
was wrong. The responses were all the same: No” (Skell, 2005, p. 10).

Decades worth of Nobel Prizes awarded for discoveries in the life sciences
falsify Dobzhansky’s third and key expectation, that nothing in biology
would make sense apart from evolution. Those awards track worldwide
progress in biology and therefore should be able to catalog amazing
evolution-based discoveries. However, the late Pennsylvania State
University professor Dr. Skell summed up the actual history of the Nobel
Prize in physiology and medicine :

"I decided to explore this further by examining the 100 Nobel Prizes in
biology-related areas over the last century. And I could not find among
them any that had been awarded the Nobel Prize for their breakthrough
discoveries that I could recognize depended upon Darwinian concepts
to design the experimental work on which their discoveries were based.
... So here again, the Darwinian theory did not provide the guidance that
was necessary for those great breakthrough discoveries (ID the Future, 2007)."


It doesn't get any clearer than that. Needless to say, all of this will
swoooosh several light years above the heads of the Evo-Faithful.

FULL ARTICLE HERE : http://www.creationresearch.org/crsq...3%20Enyart.pdf

Jorge ]]> Natural Science 301 Jorge http://www.theologyweb.com/campus/showthread.php?156347-Dobzhansky-s-predictions-flop Montañez et al. The paper. Those guys are without excuse. http://www.theologyweb.com/campus/showthread.php?156309-Montañez-et-al-The-paper-Those-guys-are-without-excuse&goto=newpost Fri, 14 Jun 2013 05:15:40 GMT This paper is online:-

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation

- and because I’d being trying to tell Jorge that the discussion section left a lot to be desired to say the least, he took off his glove and slapped my face with this;-

You either don't know what you're talking about or you do know and are being dishonest about it. Tell us all, which of these two options is it, Roland? I will graciously give
you the benefit of the doubt and say that it's the former. Jorge


It seems that Jorge is politely asking me to go beyond my assertion and back up my claim.

I’ve done a bit of this through a few posts scattered across a couple of threads. However, it’s time to collect them into one thread and extend my complaint.

I’ll drip feed my points to Jorge, in an attempt to give him a chance to reply as my make my concerns known.


Background

In a nutshell, as far as I can tell, the above mentioned paper is an attempt by Montañez et al. to show that the structure of an organism’s genome is so complex that beneficial mutations are less likely than had been previously supposed. This is because of overlapping genetic codes which means means that what will be beneficial to one code, is likely to be deleterious to subsequent codes.

Their abstract is as follows:-

Quote:
Originally posted by Montañez et al
There is growing evidence that much of the DNA in higher genomes is poly-functional, with the same nucleotide contributing to more than one type of code. Such poly-functional DNA should logically be multiply-constrained in terms of the probability of sequence improvement via random mutation. We describe a model of this relationship, which relates the degree of poly-functionality and the degree of constraint on mutational improvement. We show that: a) the probability of beneficial mutation is inversely related to the degree that a sequence is already optimized for a given code; b) the probability of beneficial mutation drastically diminishes as the number of overlapping codes increases. The growing evidence for a high degree of optimization in biological systems, and the growing evidence for multiple levels of poly-functionality within DNA, both suggest that muta- tions that are unambiguously beneficial must be especially rare. The theoretical scarcity of beneficial mutations is compounded by the fact that most of the beneficial mutations that do arise should confer extremely small increments of improvement in terms of total biological function. This makes such mutations invisible to natural selection. Beneficial mutations that are below a population’s selection threshold are effectively neutral in terms of selection, and so should be entirely unproductive from an evolutionary perspective. We conclude that beneficial mutations that are unambiguous (not delete- rious at any level), and useful (subject to natural selection), should be extremely rare.

Key words: beneficial mutation, probability, multiple codes, overlapping codes, ENCODE, poly- functional DNA, selection threshold
It’s important to note from the abstract, that the paper has nothing to do with the origin of life or DNA. It’s about the near impossibility of beneficial mutations to arise in the genome of living organisms because different genetic codes overlap.

So the authors have a problem when it comes to research papers that are purporting to demonstrate the reality of the kind of mutation they are wanting to do away with.


Example 1 - Bait and switch

In 1988, a group of scientists began what is called the E. coli long-term evolution experiment. In the tightly controlled experiment, the scientists were hoping to address several questions relating to evolution, and some interesting changes occurred which quite naturally, the researchers attributed to beneficial mutational changes.


So page 157 of the above mentioned paper of Montañez et al., you read this:-

Quote:
Originally posted by Montañez et al (bolding is mine)
The long-term E. coli experiments of Lenski et al. [58] have been widely acclaimed as “proof of evolution before our very eyes”. Such evolution would suggest that numerous beneficial mutations were arising. It is useful to examine these claims more carefully. The E. coli in these long-term experiments (which involved vast numbers of cells over vast numbers of generations), did not appear to evolve any new functions. The only changes that were observed involved adap- tations to the specific artificial growth medium. This type of adaptive change to an external factor is only a superficial improvement — it does not explain how the E. coli genome arose, nor how the information specifying the bacteria’s internal workings arose.
That bolded part is a classic bait ‘n switch.

The paper of Montañez et al. is not about addressing issues relating to the origin of life or the origin of DNA, so this objection to the results of an experiment that had nothing to do with addressing any question regarding the origin of life or the origin of DNA, is little more than a fraudulent complaint.

Their paper is about the supposed non existence of beneficial mutations, period. Lenski's experiment is about the origin of beneficial mutations.

If you cannot understand the problem here, then consider that you write a paper with the aim of showing that no athlete has run a four minute mile. You are faced with the problem then, of dealing with papers that make the claim that several athletes have indeed managed this feat. You are making a fraudulent complaint then, if you take one of those papers and object to its claims on the ground that it does nothing to demonstrate how athletics originated in the first place. The origin of athletics has nothing to do with the intent of your paper and it has nothing to do with the intent of the papers showing athletes who have run the four minute mile.



You should be ashamed of yourself for putting your name to this Jorge. What's even worse, I suspect you do this, all the while thinking that you are doing the will of God. Seemingly, however, you don't ask yourselves whether or not this kind of deceptive thinking could be the will of God? What are you trying to show to me, about the kind of a god you worship? It cannot be a God of awe, a creator God, a God of pure truth and justice, can it? Such a God would not guide believers to such deception, surely. ]]> Natural Science 301 wattsr1 http://www.theologyweb.com/campus/showthread.php?156309-Montañez-et-al-The-paper-Those-guys-are-without-excuse Next Generation Science Standards http://www.theologyweb.com/campus/showthread.php?156305-Next-Generation-Science-Standards&goto=newpost Thu, 13 Jun 2013 22:32:14 GMT For those interested in the state of K-12 science standards in the U.S. Several years ago the National Research Council, the National Science Teachers Association, the American Association for the Advancement of Science, and Achieve all recognized the need for a new set of comprehensive, up-to-date science standards for the U.S. In 2011 they began work on the *Next Generation Science Standards* (NGSS). The standards were rigorously researched and vetted, and the final product was released... For those interested in the state of K-12 science standards in the U.S.

Several years ago the National Research Council, the National Science Teachers Association, the American Association for the Advancement of Science, and Achieve all recognized the need for a new set of comprehensive, up-to-date science standards for the U.S. In 2011 they began work on the Next Generation Science Standards (NGSS). The standards were rigorously researched and vetted, and the final product was released to the public in April of 2013.

Next Generation Science Standards

From their website:

Quote:
Step One: Getting the Science Right The National Research Council (NRC), the staff arm of the National Academy of Sciences, began by developing the Framework for K–12 Science Education. The Framework was a critical first step because it is grounded in the most current research on science and science learning and identified the science all K–12 students should know. To undertake this effort, the NRC convened a committee of 18 individuals who are nationally and internationally known in their respective fields. The committee was composed of practicing scientists, including two Nobel laureates, cognitive scientists, science education researchers, and science education standards and policy experts. In addition, the NRC used four design teams to develop the Framework. These design teams, in physical science, life science, earth/space science, and engineering, developed the framework for their respective disciplinary area. A public draft was released in July of 2010. The NRC reviewed comments and considered all feedback prior to releasing the final Framework on July 19, 2011. Read more about the Framework online here.

Step Two: States Developing Next Generation Science Standards In a process managed by Achieve, states lead the development of K–12 science standards, rich in content and practice, arranged in a coherent manner across disciplines and grades to provide all students an internationally-benchmarked science education. The NGSS is based on the Framework and will prepare students for college and careers. The NGSS was developed collaboratively with states and other stakeholders in science, science education, higher education and industry. Additional review and guidance was provided by advisory committees composed of nationally-recognized leaders in science and science education as well as business and industry. As part of the development process, the standards underwent multiple reviews from many stakeholders including two public drafts, allowing all who have a stake in science education an opportunity to inform the development of the standards. This process produced a set of high quality, college- and career-ready K–12 Next Generation Science Standards ready for state adoption. The standards were published on this website when they were completed in April 2013.
Some of the key concepts from biology

Quote:
LS4.A: Evidence of Common Ancestry and Diversity
Some kinds of plants and animals that once lived on Earth are no longer found anywhere. (Note: moved from K-2) (3-LS4-1)
Fossils provide evidence about the types of organisms that lived long ago and also about the nature of their environments. (3-LS4-1)

LS4.B: Natural Selection
Natural selection leads to the predominance of certain traits in a population, and the suppression of others. (MS-LS4-4)

LS4.C: Adaptation
For any particular environment, some kinds of organisms survive well, some survive less well, and some cannot survive at all. (3-LS4-3)

LS4.D: Biodiversity and Humans
Populations live in a variety of habitats, and change in those habitats affects the organisms living there. (3-LS4-4)
The standards have already been tentatively accepted by more than half of all U.S. states with the latest being Kansas, that hotbed of Creationism.

Kansas board approves new science standards

Of course the religious right-wing nutters have been screaming bloody murder. Leading the charge is a group founded by none other that our resident YEC "scientist" Clucky Fraudandez called C.O.P.E: Clueless Oafs Panning Evolution. Sorry, that's Citizens for Objective Public Education. It's the usual Creationist BS - evolution is really a religion, teach the controversy, blah blah blah. :lol:

After a long slide towards mediocrity thank goodness the quality of science education in the U.S. is finally headed back up. :thumb:

- T ]]> Natural Science 301 Tiggy http://www.theologyweb.com/campus/showthread.php?156305-Next-Generation-Science-Standards Past leaves evidence in the present. Probably ‘twas a rock. http://www.theologyweb.com/campus/showthread.php?156262-Past-leaves-evidence-in-the-present-Probably-‘twas-a-rock&goto=newpost Mon, 10 Jun 2013 20:59:28 GMT There has been ongoing debate as to whether or not the object that hit Tunguska in Siberia over 100 years ago was a comet or a meteorite. The problem is that no eyewitness understood what it was that they saw. However, evidence from later expeditions has fueled an ongoing argument - was it a meteor, a comet or even something more exotic, like a black hole, (and perhaps something even more exotic yet, like a crashed alien space craft)? Well maybe the mystery has finally been resolved,... There has been ongoing debate as to whether or not the object that hit Tunguska in Siberia over 100 years ago was a comet or a meteorite.

The problem is that no eyewitness understood what it was that they saw.

However, evidence from later expeditions has fueled an ongoing argument - was it a meteor, a comet or even something more exotic, like a black hole, (and perhaps something even more exotic yet, like a crashed alien space craft)?

Well maybe the mystery has finally been resolved, even though no one understood what it was they had witnessed on that day, over a 100 years ago.

Rock samples suggest meteor caused Tunguska blast


The abstract and photos can be found here:-

New evidence of meteoritic origin of the Tunguska cosmic body ]]> Natural Science 301 wattsr1 http://www.theologyweb.com/campus/showthread.php?156262-Past-leaves-evidence-in-the-present-Probably-‘twas-a-rock Relativistic Doppler Effect http://www.theologyweb.com/campus/showthread.php?156251-Relativistic-Doppler-Effect&goto=newpost Mon, 10 Jun 2013 11:59:54 GMT Ok, time for some edumecation.

Last time, we explored how Einstein derived his famous equation, E = mc2
See: http://soi.blogspot.ca/2013/06/einst...-equation.html

One of those equations was taken for granted.
γB+ = ½ E(1 + (V/c)cosΦ)(1 – V2/c2)-½

At the time that Einstein published his papers in 1905, it had been derived by others, so he didn't have to do it.

In this blog, that equation is derived from first principles.

See: http://soi.blogspot.ca/2013/06/relat...er-effect.html

EDIT: no ads on that site, not trying to get more clicks. :teeth: ]]> Natural Science 301 little_monkey http://www.theologyweb.com/campus/showthread.php?156251-Relativistic-Doppler-Effect Ancient Egyptian Calendar http://www.theologyweb.com/campus/showthread.php?156217-Ancient-Egyptian-Calendar&goto=newpost Sat, 08 Jun 2013 04:28:07 GMT The ancient Egyptian calendar was split into twelve months of 30 days with an additional five days attached at the end of the year. The total number of days were exactly 365. Since our tropical year is closer to 365.24 days, commentators have said that Egypts calendar wandered and got out of sync with the seasons. Ive got a question about this. About when (what century approx) did the Egyptians get rid of this system for something more accurate? Any one know? :noid: Thanks. The ancient Egyptian calendar was split into twelve months of 30 days with an additional five days attached at the end of the year. The total number of days were exactly 365.

Since our tropical year is closer to 365.24 days, commentators have said that Egypts calendar wandered and got out of sync with the seasons. Ive got a question about this.

About when (what century approx) did the Egyptians get rid of this system for something more accurate? Any one know? :noid:

Thanks. ]]> Natural Science 301 Ged http://www.theologyweb.com/campus/showthread.php?156217-Ancient-Egyptian-Calendar Clucky and the Tooters “Creation Science” available online! http://www.theologyweb.com/campus/showthread.php?156199-Clucky-and-the-Tooters-“Creation-Science”-available-online!&goto=newpost Thu, 06 Jun 2013 22:27:11 GMT Last year about this time the Discovery Institute began crowing about their science-shaking Cornell Symposium in Biological Information and its coming publication by prestigious science publishing house Springer. The Disco Tooter crowd included the usual Creationist IDiot suspects – Behe, Dempski, Marks, Sanford, Wells, Gitt – as well as our own Clucky Fraudnandez.

Only problems were, 1) the symposium had nothing to Cornell except that’s where the Tooters rented some space, and 2) Springer had been misled into thinking this was a conference on Information Theory, a legitimate mathematical topic.

Springer soon found out the truth and canceled the publication while Cornell didn’t take too kindly to having its name associated with such pseudo-scientific claptrap and threatened heavy duty legal action. Bottom line is the Tooters took all their “Cornell” name-dropping offline beat a hasty retreat.

The events were covered in some detail here.

Symposium on Biological Information at Cornell

Now, a year later looks like the Tooters finally found someone willing to publish their garbage. According to UD the Creationist meeting papers are to be published by a Singapore based clearing house, World Scientific Publishing Company. WSPC is not known for mainstream scientific literature but handles many ‘fringe’ and vanity publications. They also don’t do scientific peer-review but only “peer-editing”, meaning they basically check papers for spelling and grammar.

They’re asking $128 for this turkey, doubly amazing when you consider they have also put all the papers online for free.

Included are such gems as Granville Sewell’s ridiculous “2nd law of thermodynamics refutes evolution” :ahem:, as well as two papers co-authored by our own Clucky Fraudnandez! Let’s take a peek.

Biological Information — What is It?
Werner Gitt, Robert Compton, Jorge Fernandez

This is just another sad retelling of the Creationist standard “DNA is a code, all codes require intelligence, therefore ID!” Clucky and Gitt use the same weasely non-definitions, make the same PRATT claim that “DNA is abstract information”. Nothing new to see here.

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation
George Montañez, Robert J. Marks II, Jorge Fernandez, John C. Sanford

This one is even dumber. The authors analogize DNA to an multi-dimensional crossword puzzle, then claim that since any one change in a letter must still work in all connecting words that beneficial mutations must be too improbable for evolution to happen. First, DNA doesn’t function that way. While some changes to DNA may prevent protein formation and be immediately fatal to an animal there are many more that are effectively neutral – the protein is still there, still working but with slightly different function. Second (and this is a killer for them) there is no such thing as an inherently ‘beneficial’ mutation. Whether a genomic mutation is beneficial can only be determined after the fact when the phenotype is subjected to selection pressure from the environment. Of course, the environment is a dynamic place and what is ‘neutral’ today could be beneficial next week, and vice versa.

I see now why Clucky and the Tooters were so hesitant to submit these to any reputable scientific journals or even put any of them online before – they may very well have been laughed clean off the planet. :no:

- T ]]> Natural Science 301 Tiggy http://www.theologyweb.com/campus/showthread.php?156199-Clucky-and-the-Tooters-“Creation-Science”-available-online! <![CDATA[Testing "Little e" and "Big E".]]> http://www.theologyweb.com/campus/showthread.php?156198-Testing-quot-Little-e-quot-and-quot-Big-E-quot&goto=newpost Thu, 06 Jun 2013 21:32:02 GMT Hi folks This brief essay has to do with a pet peeve of mine - about macro vs micro evolution, observation, past process, present process, science truthly called, and YECs who rage against Christians for accommodating Genesis 1 with the science of fallible humans, but who happily accommodate other Biblical verses with the science of fallible humans. The essay has to do with a couple of interesting papers, papers that are connected, and which deal with modeling tooth development, growth... Hi folks

This brief essay has to do with a pet peeve of mine - about macro vs micro evolution, observation, past process, present process, science truthly called, and YECs who rage against Christians for accommodating Genesis 1 with the science of fallible humans, but who happily accommodate other Biblical verses with the science of fallible humans.

The essay has to do with a couple of interesting papers, papers that are connected, and which deal with modeling tooth development, growth and evolution.

But first a bit of background.


BACKGROUND

From time to time posters will mention the word “macroevolution” or they will post an item which is concerned with macroevolution - namely speciation or speciation going so far as to produce new genera, families etc.

Inevitably such a bold move by an innocent poster will bring on what is seemingly a godly wrath and a great yapping about how macroevolution is not science and this is “fact, Fact, FACT”. Lately, macroevolution has been classified as “Big E” with the claim that accepting it is nothing more than religious faith, a devilishly inspired religious faith. This is notwithstanding the fact that one can get as awful lot of evidence for its reality from a text such as 29+ Evidences for Macroevolution: The Scientific Case for Common Descent

In the ensuing rant, the poster appears to accept some kind of godly evolution which seems to be nothing more than an odd bit of local variation within species, and because it’s acceptable, it is classified as “little e”. Supposedly, little e, unlike Big E, is observed. Well, so it is asserted.

Various reasons for this hatred of Big E have been proffered over the years. If my understanding is correct, these reasons range from Big E not being metaphysically neutral, to Big E not being observable.

These reasons, which have arisen from years of Deep Thought, don’t make much sense. For example, many Bible verses show that such mundane things as rainfall and frost, or the formation of babies in the womb cannot be metaphysically inert. The claim is made that God does these things. Hence why is there not a “Big M” for meteorological science which claims that frost, rain, and babies are natural processes - in contradiction to the Bible, and a “little m” - for meteorological theories dealing with phenomena which do not clash with Biblical text?

And besides, if direct observability is the problem, then most of science does not count as such, not even the little e. After all, who has directly observed variation in the wild, such that they can rule God out, and natural process in?

Any way, I present two interesting papers dealing with Big E and little e.

They are connected in that the first is about using a computational model to understand how teeth form and vary within and between individuals. The second then uses that model to understand how development constrains evolution, particularly in the case of evolution across various taxonomic classifications.


THE PAPERS

LITTLE e, THE MODELING OF HOW TEETH FORM AND VARY BETWEEN INDIVIDUALS.

Three years ago A computational model of teeth and the developmental origins of morphological variation was published in Nature

In the paper, the authors describe how they developed a simple computational model that quite accurately shows how mammalian teeth develop in the jaw of a growing embryo. Their model relied on an interaction of cellular signals diffusing across the region of the developing tooth. The signals either up regulated or down regulated various growth factors and their interaction went a large way to determining tooth form. The other factor they included was the physical environment. Stresses and strains brought on within the growing system as cells physically interact between themselves and their environment also determined the final outcome. As the authors write (bolding is mine):-

Quote:
Originally posted by link above
The relatively well-studied mammalian tooth is suitable for identifying the developmental principles linking genotype to phenotype. Cusps constitute the major morphological features of teeth, and cusp shape, size, position and number are used to differentiate taxa. At the onset of each cusp formation—non-dividing epithelial signalling centres—the secondary enamel knots appear17. Experimental evidence from mouse molars implicates molecular signalling in activating and inhibiting the formation of enamel knots11, 18, and computational modelling of these dynamics can account for basic aspects of tooth formation19. Previous models19, 20, however, approximate tooth shapes without detailed implementation of the mechanical properties of cells. Because mechanical forces have a central role in tissue architecture20, 21, 22, 23, here we have constructed a model integrating experimentally inferred genetic interactions with tissue dynamics (Fig. 1a), thereby allowing us to study population-level multivariate variation.
So the advance the authors are claiming, is to have integrated environmental forces with genetic interactions to better understand how teeth form and how they can vary within the jaw of an individual, and how they can vary between the organisms within a population.


BIG E AND THE MODELING OF MACROEVOLUTION

Naturally, most folk “in the know” think that the process that drives little e, if operated for long enough, would bring about the changes we label here, as Big E. (In fact, one major creationist organisation appears to accept this kind of thinking these days. Answers in Genesis for example, appears to accept that speciation does happen and that enough of it can bring about the appearance of new genera, and even new sub families, if not new families. If you read some of their articles, they appear to accept almost any evolutionary change, as long as it’s not “molecules to man evolution”.)

So, keeping the above in mind, roll forward three years. In a very recent Nature we find Adaptive dynamics under development-based genotype–phenotype maps

In this paper, the authors (one of whom contributed to the research mentioned above), describe how they took the model developed above, and extended its use to understand an aspect of the process leading to macroevolution.

In essence, the model is used to determine how development constrains evolution. As a News and Views commentary in Nature describes it:-

Quote:
Originally posted by link above (bolding is mine)
The evolutionary biologist Leigh Van Valen famously defined evolution as the control of development by ecology1. By this, he meant that evolution is governed by the fitness of the phenotype of an organism (its physical form); that fitness depends on the ecological context in which the phenotype exists; and that an individual's phenotype is not a static structure built directly from genes, but a dynamic structure that unfolds sequentially from fertilization to adulthood. The developmental sequence determines and constrains which phenotypes can emerge, such that evolutionary change depends on modifications to development. On page 361 of this issue, Salazar-Ciudad and Marín-Riera2 present a groundbreakingly realistic computational model of this process. They use their model to demonstrate that developmental complexity often prevents natural selection from reaching optimal fitness when fitness is directly linked to attaining a particular phenotype, but that these 'adaptive peaks' can be reached when fitness is instead linked to functional properties of the phenotype*.
In essence the researchers used the model of tooth formation and mutated it, by randomly changing model parameters. They determined fitness by measuring the outcome against some predetermined tooth shape (an ideal shape, the top of the fitness peak), or by measuring it against some function. That is, fitness was measured against the optimal shape to (say) crack open a nut, or fitness was measured against a function, that is, any function that will crack open a nut.

It was there that the surprise came. When fitness was measured against some optimal tooth shape, evolution was unlikely to reach the optimum. Even when it did reach the optimum, it only did so when the simulation began with shapes relatively close to that ideal. As the News and Views article puts it, they think this “is due to the complexity of developmental interactions; the sequence of parameter changes that is needed to generate the optimum phenotype includes changes that temporarily reduce fitness, but selection prevents these changes from occurring, and thus prevents the phenotype from evolving to the adaptive peak.”.

On the other hand, if fitness was measured against functional properties, then the adaptive ideal was most often reached. The News and Views article describes it thus - “This is because many different phenotypes can have the same functional properties9 — a herbivorous mammal, for example, simply needs grinding and chewing surfaces on its teeth, regardless of how the surfaces are constructed. Thus, there are many more paths to a functional adaptive peak than to a phenotypic one, especially for a phenotype that has a complex developmental system, such as a tooth.”

As the News and Views concludes:-

”Salazar-Ciudad and Marín-Riera's results reveal a lot about how evolution may work in practice. The originality of their work lies in how the model realistically maps the interactions between genetic parameters, developmental processes, adult phenotypes and functional properties. These interactions introduce dynamic properties that allow for morphological transitions and evolutionary novelties that were not captured by earlier computational models of the evolution of complex phenotypes10. The authors' results highlight interesting questions. If phenotypic evolution is likely to get stuck on suboptimal adaptive peaks, what happens to the evolving populations? Do they simply persist in a suboptimal state? Do their ecological relationships change to fit their phenotype, thereby creating new adaptive peaks? Or do they become extinct as they are out-competed by populations that can reach a more optimal phenotype? Salazar-Ciudad and Marín-Riera's focus on teeth — which can be studied empirically in living populations, among distantly related clades and in the fossil record — offers considerable potential for testing their evolutionary predictions and closing the knowledge gaps between genetics, development and macroevolution.”



CONCLUSION

Anyway, I thought I would bring these articles to your attention. Unfortunately they are behind paywalls. If you can get to them however, they provide an interesting insight into the nature of science and how researchers test their ideas - in the first instance, ideas about how teeth form, grow and vary, and in the second instance, how they evolve across the taxa.

In both cases, it’s science that is being done. The microevolution of the first paper is as unobservable as is the macroevolution of the second paper. After all, to use two commonly made creationist arguments:-

1) Who was there to observe any animal in the wild, micro evolve, such that God can be ruled out and nature ruled in?

2) And what does a laboratory experiment prove? It proves that an intelligent designer was behind it. Hence all the first experiment demonstrates is that the intelligent designer must be as much behind little e as the ID is behind Big E.

And then there is the third point to be made, in the context of Biblical infallibility and YEC insistence on a wooden, literal interpretation of Gen 1:-

3) Verses across the Old Testament tell us that we know nothing about how babies form and grow, because God does it all (Ps 139:13, Ecc 11:5 and Isa 44:24). Clearly that first paper disagrees with this Biblical assessment. And if the appeal is made that culture and time must be brought in to account for the claims of those Biblical verses, then equally it should be brought in to account for Genesis. YECs cannot have it both ways. Well they can, but it makes no logical sense.


Inference is a valid mode of reasoning. All scientific fields rely on it. The past does leave evidence in the presence for us to observe, just like unobservable processes acting now, leave evidence for us to observe. These observations, allow us to test our ideas about the past, and our ideas about unobservable processes operating now. And as the above papers show, various observations made in the laboratories now, about processes that are essentially invisible as they unfold, allow us to test both micro and macro evolutionary concepts.

And they also allow us to test our ideas on how cells interact to bring about the formation of things such as teeth. After all, we don’t actually directly see cells pumping out signaling molecules which make other molecules join together to make teeth. These are just models scientists think up in order to understand what it is they can observe.

And as I point out above, the Bible has a very different take on why teeth grow. Interacting cells and mechanical stress, have nothing to do with it. ]]> Natural Science 301 wattsr1 http://www.theologyweb.com/campus/showthread.php?156198-Testing-quot-Little-e-quot-and-quot-Big-E-quot <![CDATA[Darwin Dodo's ...]]> http://www.theologyweb.com/campus/showthread.php?156186-Darwin-Dodo-s&goto=newpost Thu, 06 Jun 2013 15:09:01 GMT http://crev.info/wordpress/wp-conten...arwinDodos.jpg

Nature’s editorial for May 15, “Science in schools,” took aim at
Creationists. They did this as a sort of commemoration of Eugenie Scott’s
retirement from the National Center for Science Education. Hehe - this
send-off was so very appropriate, kind'a reminding us all what the NCSE
is truly about.

Scott has returned to her coven where she will live blissfully with her cats,
bats and rats. Be-gone witch ... good riddance!!! [Unfortunately, there is
an endless supply of them ... ]


Back into "exile" I go .................... :read:

Jorge ]]> Natural Science 301 Jorge http://www.theologyweb.com/campus/showthread.php?156186-Darwin-Dodo-s Cambrian biota and precursers - further discussion http://www.theologyweb.com/campus/showthread.php?156096-Cambrian-biota-and-precursers-further-discussion&goto=newpost Sun, 02 Jun 2013 11:21:58 GMT Jorge posted this in the YEC Fossils thread and I think it's something worth discussing on it's own so I'm going to cut and paste his post in it's entirety and then link to some responses in the other thread to get the conversation started in this one.

Quote:
Originally posted by Jorge View Post
Correct. You wanna see these people tremble? Talk about the Cambrian 'Explosion'!

In the Cambrian layer, millions of fossils have been found. They have been classified
into a relatively small number of general body plans - the same body plans that we
find today!

Here's the thing - they have NEVER found either in the Cambrian or Pre-Cambrian
layers an "intermediate" form leading to those body plans. They just appear -
POOF! - as if already created in place. Hmmm ... where have I heard that before? :huh:
I digress ...

Then, to defend their Sacred Cow, they've concocted auxiliary hypotheses (a.k.a.
cheap excuses). One of these is that, "The evolutionary precursors were soft-
bodies and because of this none were preserved."

Yeah, right ... "Trust us, it happened only the evidence is gone ... but trust us."

In any event, that cheap excuse 'scientific hypothesis' was shot to pieces with
subsequent findings that have been amply confirmed and reported in their
Sacred texts such as Science and Nature and others.

Lastly, another one of their dirty tricks is this: they find fossil A - dated
to 250 MYA (by their methods). They find fossil R - dated to 100 MYA.
Then they say, "A is the ancestor of R. B, C, D, E ... P, Q are "somewhere"
in the Earth, we just haven't found them yet."

Yeah, right ... "Trust us, it happened but we haven't found the evidence ... trust us."

These are just some of the extremely dishonest games that these people play.
In the meantime, people's faith in God and their lives get destroyed.

Jorge
]]> Natural Science 301 USIncognito http://www.theologyweb.com/campus/showthread.php?156096-Cambrian-biota-and-precursers-further-discussion <![CDATA[Einstein's Derivation of the Famous Equation, E=mc2]]> http://www.theologyweb.com/campus/showthread.php?156081-Einstein-s-Derivation-of-the-Famous-Equation-E-mc2&goto=newpost Sat, 01 Jun 2013 08:57:31 GMT Quite surprisingly, you just need ordinary algebra, no calculus, no tensors to scare the hell out of you. Enjoy. http://soi.blogspot.ca/2013/06/einsteins-derivation-of-famous-equation.html Note: no ads, not trying to get more clicks, :-D Quite surprisingly, you just need ordinary algebra, no calculus, no tensors to scare the hell out of you.

Enjoy.

http://soi.blogspot.ca/2013/06/einst...-equation.html

Note: no ads, not trying to get more clicks, :-D ]]> Natural Science 301 little_monkey http://www.theologyweb.com/campus/showthread.php?156081-Einstein-s-Derivation-of-the-Famous-Equation-E-mc2 <![CDATA[Is Newton's Law of Gravity Valid Within General Relativity]]> http://www.theologyweb.com/campus/showthread.php?156041-Is-Newton-s-Law-of-Gravity-Valid-Within-General-Relativity&goto=newpost Thu, 30 May 2013 10:09:30 GMT Some people have made the claim that Einstein proved that Newton was wrong on gravity. Well, no exactly. Einstein showed that his field equations in General Relativity at low gravity and low velocity yields Newton's Law of Gravity. This is a one of the great calculation performed a 100 years ago by the man whose name is synonymous to genius.

Enjoy.

http://soi.blogspot.ca/2013/05/is-ne...lds-valid.html ]]> Natural Science 301 little_monkey http://www.theologyweb.com/campus/showthread.php?156041-Is-Newton-s-Law-of-Gravity-Valid-Within-General-Relativity Ahhh!!!! RATS on Mars!!! http://www.theologyweb.com/campus/showthread.php?156021-Ahhh!!!!-RATS-on-Mars!!!&goto=newpost Wed, 29 May 2013 16:47:54 GMT http://www.foxnews.com/science/2013/05/29/mars-rat-spied-by-nasa-curiosity-rover/ Eeeeeeeek! http://www.foxnews.com/science/2013/...riosity-rover/

Eeeeeeeek! ]]> Natural Science 301 DesertBerean http://www.theologyweb.com/campus/showthread.php?156021-Ahhh!!!!-RATS-on-Mars!!! Dawkins exemplifies Atheists - for fun http://www.theologyweb.com/campus/showthread.php?155987-Dawkins-exemplifies-Atheists-for-fun&goto=newpost Sat, 25 May 2013 12:03:23 GMT Atheists ... ya got'ta 'love' their wackiness .......... :lol:


"The fact that life evolved out of nearly nothing, some 10 billion years
after the universe evolved out of literally nothing, is a fact so staggering
that I would be mad to attempt words to do it justice."
—Richard Dawkins


Thank You, Richard.....

Thank you, Richard, you have helped us
Know that Nothing brought you here...,
Thank you, sir, for nothing really,
That you've made so crystal clear.

Thanks for trying to do justice,
To a thought so amply lame...
Thanks for giving us a glimpse, sir
To ideas quite inane.

Thank you for this deep, deep wisdom,
Thanks for helping us to see!
Thanks for helping us to ponder
Such in-depth vacuity.

Thank you for the vain attempt, sir,
To make nonsense seem so keen.
We are staggered by your insight,
Sadly, we see what you mean!

Yes, we thank you for the madness,
You have brought here to the plate.
We commend you for the effort....
Oh, so richly profligate!

SOURCE : http://www.tomgraffagnino.com/though...u-richard.html

Jorge ]]> Natural Science 301 Jorge http://www.theologyweb.com/campus/showthread.php?155987-Dawkins-exemplifies-Atheists-for-fun <![CDATA[Another example of the 'Spin-Science' of the Evo-Flock]]> http://www.theologyweb.com/campus/showthread.php?155982-Another-example-of-the-Spin-Science-of-the-Evo-Flock&goto=newpost Fri, 24 May 2013 16:54:56 GMT A recent article presents an observation : certain 'mutant' cockroaches have
evolved so that they will reject the sweet glucose that is often used as bait to
coat the poison. The "obvious conclusion", say the Evo-Flock, is that we are
seeing evolution in action, a new type of cockroach - a 'mutant'- has 'evolved'.
These results were reported in Science.

Here's the crux of the whole thing - the bolds are mine to accent the point:

"Usually, when natural selection changes taste abilities, it simply makes
animals more or less sensitive to certain taste types.

"For example, bees that specialise on collecting nectar are less sensitive
to sugar than other bees, which means that they only collect concentrated
nectar. Evolution has made sugar taste less sweet to them,
but they still like it.

"In the cockroach case, sugar actually tastes bitter - an effective way for
natural selection to quickly produce cockroaches that won't accept the
sugar baits that hide poison."

Dr Schal said this was another chapter in the evolutionary arms race
between humans and cockroaches.

"We keep throwing insecticides at them and they keep evolving mechanisms
to avoid them," he said.

Let me now concisely and scientifically analyze the same observations
WITHOUT the Evolutionary goggles.

The cockroaches Evolved NOTHING! Natural selection changed NOTHING!
There was no "Evolution" of special taste receptors in these 'mutant'
cockroaches. Here's what is actually going on:

There is inherent variation in all living things. This variation is manifested
in both the genotypes and the phenotypes. Some humans, for example, have
longer legs, some have shorter; some have longer fingers than others, eye
color differs, fingerprints are different ... etc ... etc. We also have different
tastes - one person will love spinach while another person is repulsed by it.
Some people love peanuts; others are violently allergic to peanuts (recently
a man in his 20's died by eating a cookie that contained peanuts).

So, suppose you have a population of 1,000,000 cockroaches. Out of those,
999,900 love sugar and so, when they eat the sugar-coated poison, they die.
But 100 of these roaches (0.01% of the population) had a natural distaste for
sugar and so they 'spat out' the sugar and did not ingest the poison.

These went on to reproduce. Their natural aversion to sugar was passed on
to their offspring. The next generation had MOST of the population with
this natural 'intolerance' / 'distaste' for sugar. That's it. NOTHING "Evolved"!

The Evo-Flock, always seeking to prop-up their ridiculous myth with
pseudo-evidence, interpret what just happened as "Look, the cockroaches
EVOLVED so as to avoid the poison." Yeah, right. Unadulterated
BS fed to the masses as part of the relentless Evo-propaganda.

CONCLUSION : Same observations, different interpretations - a lesson
that will undoubtedly be missed by the Evo-Flock here at TWeb.

If you're going to criticize my post, be sure to stick to SCIENCE -
I really do not want to hear your Evo-Faith disguised as science.

One last comment : even if a change had occurred (it didn't!) in
the cockroaches genome, the 'mutant' cockroach remained - what
else? - a cockroach. The Evo-Flock is still searching for the mythical
example of a macro-change. Nonetheless, their Faith remains unshaken. :smile:

ARTICLE HERE : http://www.bbc.co.uk/news/science-environment-22611143

Jorge ]]> Natural Science 301 Jorge http://www.theologyweb.com/campus/showthread.php?155982-Another-example-of-the-Spin-Science-of-the-Evo-Flock