matt8819 wrote:So in other words, someone more knowledgeable than you tells you what you got wrong, you claim victory in some bizarre bastardization of logic so new we don't yet have a name for how wrong it is?

matt8819 wrote:So in other words, someone more knowledgeable than you tells you what you got wrong, you claim victory in some bizarre bastardization of logic so new we don't yet have a name for how wrong it is?

Atheistoclast wrote:

matt8819 wrote:So in other words, someone more knowledgeable than you tells you what you got wrong, you claim victory in some bizarre bastardization of logic so new we don't yet have a name for how wrong it is?

He got his Master's in geography and doesn't understand jack shit about molecular biology beyond the buzz words.

Summary: This paper is fatally flawed in numerous ways. I illustrate in detail below.
MAJOR PROBLEMS
PROBLEM #1: UNSUPPORTED ASSERTIONS ABOUT "ESSENTIALLY UNSOLVED" PROBLEMS IN EVOLUTIONARY
BIOLOGY
"While it is absolutely correct that evolutionary biology per se is entirely uncontroversial within science, and is not
in any way disputed by the great majority of researchers, many important areas of the theory do remain very
controversial and have certainly not been settled. In particular, the origins of complex structures and systems, the
creation of biological information, developmental evolution and morphogenesis remain essentially unsolved."
This statement is untrue. For example, the origin of new genetic information is explained by the well-known process
of gene duplication followed by one or more rounds of mutations (of various well-known sorts) and selection. New
genes with modified sequences and different functions are new information on any reasonable criterion of what
"information" means.
Required references, which would have to be argued with in detail to have even a hope of making a successful
contrary argument:
1. Long et al. (2003). The origin of new genes: glimpses from the young and old. Nature Reviews Genetics
(20+ examples of the origin of new genes, some of them in which the origins are known in much detail, although a
few need updates due to newer research.I am unconvinced by the claim of a new plant plasmid gene that is a
chimera due to lateral gene transfer, this is likely just an artefact of the phylogenetic analysis of the original paper,
which I have looked at.
2. R Ponce, DL Hartl (2006). a.oeThe evolution of the novel Sdic gene cluster in Drosophila melanogaster.: Gene
376(2), 174-183.
The novel gene Sdic explained in great detail.
The above problem with the information argument stands despite the endless arguments of creationists and a few
other cranks. I have extensive experience with this literature, and it always boils down to use of a subjective and
inconsistent definition of "information", which is then employed to avoid all of the obvious and overwhelming
counterexamples, like those mentioned above (although the mass of counterexamples is virtually always not even
cited, itself an unforgivable scholarly mistake).
Although this ambiguity is often concealed with a great display of technical-sounding language about information
theory, they can typically never explain why, for instance, the origin of Sdic or Jingwei is not an example of the
natural origin of new genetic information.
Bozorgmehr (2010; http://onlinelibrary.wiley.com/doi/10.1 ... 20365/full ), cited in this article, *does*
review some of the well-known cases where new genes have originated recently, e.g. Sdic and Jingwei.but even
Bozorgmehr, despite some minor quibbles in places, is forced to concede that it looks like natural evolutionary
processes have successfully produced these new genes!
In fact, they are new information even on Bozorgmehr's own personal definition of "information", as he defines it
thusly: "Therefore, I have decided to define any gain in exonic information as: 'The qualitative increase in operational
capability and functional specificity with no resultant uncertainty of outcome.'" Typically in the cases of these new
genes, the ancestral gene(s) are retained, and the new gene has a new function and new expression pattern (at least
as far as we can tell, given that we don't always know the exact function of a new gene). All of the old genes + a new
gene with new information = more information than you had before. That is GAME OVER for the "natural evolution
can't produce new genetic information" argument.
This is the case even if new genes typically lose some exonic material during their evolution. All of the old genes + a
*shorter* new gene with new information STILL equals more information than you had before.
Bozorgmehr (2010), after reviewing a bunch of cases of the origin of new genes and more-or-less admitting that
natural evolutionary processes have produced them, writes a very puzzling conclusion that basically says "Never
mind that all of these new genes evolved and their evolution can be reconstructed in some detail even with the
limited information available in the 21st century with only a small proportion of species sequenced; I'm going to
make a wild assertion that the origin of information is still a mystery."
E.g., in the conclusion of Bozorgmehr (2010), he writes,
"The various postduplication mechanisms entailing random mutations and recombinations considered were
observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of
generating genuinely distinct and entirely novel functionality."
Here, Bozorgmehr (2010), like many creationists and similarly uncritical and uninformed critics, moves the
goalposts for evolutionary theory. No longer is the goal just "new information", it is "entirely novel functionality".
But this new line that evolution has to cross has many problems:
(a) it is not rigorously defined.the reader has no way of knowing what evolutionary demonstration would satisfy
Bozorgmehr. He could always just move the goalposts again and say, "Oh, that wasn't *entirely* novel."
(b) As many, many biologists have observed and written (notably Darwin, Mayr, Gould, etc.), virtually any feature in
biology that one examines is not "entirely novel".it is a modified version of something else. Was the origin of the
mammalian middle ear "entirely novel"? No, actually we know that the middle ear evolved from modified jawbones.
How about the origin of the jaw? No, it traces back to the gill arches of early chordates. How about vertebrate
wings? Modified forelimbs. The archaeal flagellum? A modified Type 4 secretion system. The bacterial flagellum? A
modified Type 3 secretion system (although it may or may not be sister to known, modern nonflagellar T3SS; the
phylogeny here is unresolved), together with a number of other proteins coopted from nonflagellar systems (e.g.,
MotAB are homologous to TolQR and ExbBD).
This is a ubiquitous and extremely well-confirmed pattern across biology, it doesn't just apply to recently-evolved
new genes. One cannot just insert a dubious hidden premise into an argument, like the idea that "entirely novel
functionality" is ubiquitous in evolution and needs to be explained by normal evolutionary mechanisms, without an
extensive justifying argument. Well, you can do it, and you might even get it past some reviewers, but it is mere
rhetorical posturing and not a coherent argument. It is not the kind of thing that will change the minds of experts in
the field who know that virtually every complex system in biology appears to be a modified version of something
else.
PROBLEM #2
Another example.the "origins of complex structures and systems" is actually reasonably well-understood in many
cases. The only problem is that antievolutionists ignore the relevant literature, as is being done by Bozorgmehr in
his paper here. No scientific paper can claim the opposite without responsibly addressing the relevant literature,
which has been laid down in front of the antievolutionists many, many times, for example, here:
===============
Scott, E. C., and Matzke, N. (2007). "Biological design in science classrooms." Proceedings of the National Academy of
Sciences. 104(suppl. 1), 8669-8676.
http://www.pnas.org/content/104/suppl.1/8669.full
[...]
The ID movement's common claim that evolution cannot produce gnew genetic informationh is contradicted by
numerous papers documenting the origin of new genes (e.g., ref. 32) or even entire multiprotein catabolic pathways
for artificial compounds that humans have released into the environment in recent decades (33, 34). Behe's claim
has been rebutted in general (35-37) and for specific complex systems such as bird wings (38), the vertebrate blood
clotting cascade (39), the vertebrate immune system (40), and the ID movement's favorite system, the bacterial
flagellum (23, 41, 42).
23. Pallen MJ, Matzke NJ (2006) Nat Rev Immunol 4:784.90.
[...]
33. Johnson GR, Spain JC (2003) Appl Microbiol Biotechnol 62:110.123.
34. Copley SD (2000) Trends Biochem Sci 25:261.265.
35. Miller KR (1999) Finding Darwin's God: A Scientist's Search for Common
Ground Between God and Evolution (Cliff Street Books, New York).
36. Thornhill RH, Ussery DW (2000) J Theor Biol 203:111.116.
37. Matzke NJ, Gross PR (2006) in Not in Our Classrooms: Why Intelligent Design Is
Wrong for Our Schools, eds Scott EC, BranchG(Beacon Press, Boston), pp 28.56.
38. Gishlick A (2004) in Why Intelligent Design Fails: A Scientific Critique of the New
Creationism, eds Young M, Edis T (Rutgers Univ Press, New Brunswick, NJ),
pp 58.71.
39. Davidson CJ, Tuddenham EG, McVey JH (2003) J Thromb Haemost 1:1487.1494.
40. Bottaro A, Inlay MA, Matzke NJ (2006) Nat Immunol 7:433.435.
41. Miller K (2003) in God and Design: The Teleological Argument and Modern
Science, ed Manson N (Routledge, London), pp 292.307.
42. Musgrave IF (2004) in Why Intelligent Design Fails: A Scientific Critique of the
New Creationism, eds Young M, Edis T (Rutgers Univ Press, New Brunswick,
NJ), pp 72.84.
================
In the face of all of this, I have never seen an example of an antievolutionist doing any better than a sputtered "well, I
just don't believe it". It is only very occasionally that one can get them to read the literature at all, and even then I've
never seen them deal with this research in the responsible, academic way that science absolutely requires.dealing
with the facts rather than dismissing them, and proposing a more explanatory, more testable explanation.
PROBLEM #3: QUOTE-MINING
Monteiro and Podlaha (2009) state that, a.oethe genetic origin of new and complex traits is probably still one of the
most pertinent and fundamental unanswered questions in evolution today.:
The reference here is:
Wings, horns, and butterfly eyespots: how do complex traits evolve?
Bozorgmehr is misusing this paper, which I have read. The paper is devoted to testing several already existing,
already known-to-be plausible explanations for the origin of complex traits and complex developmental gene
networks. These are all just sub-hypotheses for one of the well-known and long-established general explanations of
new complex traits, known as cooption or exaptation (see Mayr 1960, cited in Scott & Matzke; and of course this
explanation goes back to Chapter 6 of Darwin's Origin of Species, which Bozorgmehr mentions but does not grapple
with.like virtually all). Cooption, in turn, is one of several specific evolutionary hypotheses that may be employed
to explain complex traits within the general hypothesis that the complex trait evolved via descent with modification,
with natural selection as a major force.
To wit, the authors write, "Here we propose an empirical test that will help distinguish instances of gene network cooption
from de novo network evolution."
Both are plausible, although they suggest (and I and most biologists would likely agree) that gene network co-option
is more likely to be the more common explanation, and it is debatable whether or not even the very limited dramatic
language that the authors use is warranted (such phrases are common in scientific papers, as papers are much less
interesting to editors if you play up the significance of what you are doing, rather than play it down). But either way,
"unanswered question" does not equal "evolution in crisis" or whatever. It is clear that Bozoghmehr isn't arguing for
teaching students about two sub-hypotheses of cooption in high school biology, he wants them to be taught e.g. that
common ancestry might be wrong, which is scientifically unwarranted, undoubtedly therefore would happen for
religious motivations only, and thus would be unconstitutional as well as poor education.
PROBLEM #4: BEGGING THE QUESTION
"Science is supposed to be a pluralistic enterprise, inclusive by its very nature, welcoming virulent debate and
arousing the deepest sense of curiosity in those pursuing it. Without continually raising objections, it is impossible
the test the worth and resilience of an idea. This is what differentiates science from dogma."
As Carl Sagan once said, the openness of science has to be coupled with very skeptical critical scrutiny. Every aspect
of modern evolutionary theory is continually being poked, prodded, and tested by evolutionary biologists in the field,
in museums, and in the lab. Many of these investigators are tenured professors who face no danger to their salary or
employment if they were to dissent from the consensus.indeed, many of them (like Gould) have launched various
mini-revolutions within the field, and furthermore, they all know that worldwide fame and credit would accrue to
someone who could come up with a better overarching theory than the theory of evolution. And yet, despite all of
this testing and motivation to overturn orthodoxy, it hasn't been done. All the experts still agree on common
ancestry, on natural selection as an important force, on the ability of natural forces like selection to produce
complexity, etc. The fact that there are debates (minor debates in the grand scheme of things) about all sorts of
details does not contradict this big picture. All active sciences have innumerable such debates going on. That is how
we move from ignorance to knowledge.
The kinds of criticisms that Bozorgmehr is talking about, though.those that suggest that evolution is just wrong,
that the origin of complex structures, of information, etc. is a complete mystery and/or requires a miracle.these
come from the absolute fringes of the biological field, if one is speaking very generously, and if one is speaking fairly,
they are coming from cranks far removed from the actual data and practices of the actual science of evolutionary
biology. Fair-mindedness does not mandate the inclusion of crank science, done with poorly-informed, half-baked
arguments by armchair critics, in scientific debate. Peer-review mostly excludes crank material from the scientific
literature, although peer-review occasionally fails.
Even if we were to include crank arguments in scientific journals, this would still beg the question of whether or not
it deserved serious discussion in **introductory biology classes in high schools**. There are a million-and-one
topics, just in biology, that don't get mentioned in high schools, purely because introductory classes have to have
introductory material, biology is a huge discipline, and there is very limited time amidst all of the other classes
students have to take. Even in an ideal situation, students are unlikely to get more than a few weeks devoted to
evolutionary theory. What should be cut, to include the crank material that Bozorgmehr would like educators to
include?
Furthermore, Bozorgmehr's criteria.any topic that gets into a peer-reviewed journal, whether legitimately or not,
whether it is being miscontrued or not, deserves to be included in introductory science classes.would lead to
complete chaos if consistently employed. Bigfoot and other forms of cryptozoology, astrology, homeopathy, cold
fusion, and numerous other forms of pseudoscience have a tiny-but-nonzero presence in the peer-reviewed journals.
Some of this is crank journals, some of this is cranky editors, some of this is cranks resubmitting articles to journals
until they catch an obscure journal with an editor or reviewer having an off-day, and some of this is mistakes due to
optimistic statistical analysis or fluke instances of statistical significance, which will happen by chance quite often.
Should all of this junk be taught in the public schools, just because it is "in" the peer-reviewed literature?
Bozorgmehr's argument would suggest this. To reach an alternative conclusion, he would have to present a
philosophy of education that somehow included fringe antievolution arguments but excluded all of the other fringe
and crank pseudoscience that is out there. I wish him luck, but he has not even attempted this task here.
My philosophy of education is that students deserve to learn the *best* and *most important* science that is
available, scaled to be age-appropriate of course. This includes major organizing explanatory theories like evolution,
and ideas that are driving the forefront of science, again like evolution. Including poorly-supported crank criticisms
of dominant theories, even those derived from the peer-reviewed literature (technically, the dark dregs of the peerreviewed
literature) does not fit with this vision.
If the crank criticism actually is correct, the proper way to promote it is *not* to try to coral the power of the
government to promote your fringe idea in the introductory classes in the public schools. The dissident's *only* job
should be to attempt to convince the relevant scientific community. That's what academia and scientific
communities are *for*.
OTHER PROBLEMS
I have already dealt with the content of Bozorgmehr (2010). It is also worth pointing out that Bozorgmehr
apparently submitted to and was rejected by a large number of journals before getting accepted (according to
discussions I have seen on the internet, where he inhabits various creation/evolution forums under the name
"Atheistoclast".
It is also worth noting that there are peer-reviewed journals and peer-reviewed journals. The journal "Complexity"
is an online-only (as of 2011) journal, outside of the field of biology, with a below-average impact factor (stats below:
mean of 500 random impact factors I downloaded from ISI's 2010 Journal Citation Reports:
(the first 500 in the JCR list; the max download size is 500)
2.112799
Nature's IF
36.101
Science's IF
31.364
PNAS
9.771
mean of the top 500 impact factors I downloaded from ISI's Journal Citation Reports:
10.16963
Complexity
1.367
*Even* an article in a top journal wouldn't really establish that a particular topic is worthy of inclusion in
introductory science classes. Nature published "memory water", Science recently published the incorrect reports of
arsenic-DNA, PNAS has had various crank contributions published by a sometimes-eccentric NAS member like Lynn
Margulis, etc.
Peer-review only *starts* with review at the journal. If an article is published, it gets processed by the scientific
community. Sometimes the status of the article goes up; often, the status of the article goes down; very often, the
work is ignored. Students deserve to get the best stuff, not "all the stuff" (as if the desire for "teach everything"
wasn't a cheap rhetorical ploy in the first place, designed to provide cover for "teach crank antievolutionary stuff!").
Other notes on cited articles and other assertions:
Behe (2010), like Bozorgmehr, reviews a number of cases where evolution (lab evolution, in Behe's case) is shown
able to produce new biochemical functions, the ability to process new food sources, and the like. But then he sets up
some new, arbitrary, more obscure "line in the sand" for evolution, and then claims that evolution is unable to cross
*that* line.never mind that the line was set up to be just outside the capabilities of what simple lab experiments
(short time periods, simple selection forces, simple environments, clonal populations) can observe. It is like saying
in 2005 that "current extrasolar planet detection techniques have only detected gas giant planets, therefore smaller
planets don't exist."
Lambert (1984) is pointless to cite, as the DNA/protein "chicken and egg" problem was solved in the mid-1980s by
the RNA World hypothesis.
Re: Kitzmiller.the lack of peer-reviewed literature was only one of many problems with ID. And the ID guys did
introduce various things that they *claimed* were peer-reviewed literature (much of this is in the DI list that
Bozorgmehr cites).but it all fell apart on cross-examination, or, often, wasn't introduced in the first place, for fear of
cross-examination, despite being cited in expert reports. Philosophy journals, review articles, articles by ID
personalities but that don't mention ID, claims that are directly contradicted by data, etc. .none of this adds up to a
record of empirical research literature. And, of course, even having such a record is a long, long ways from being
"the *best* and *most important* science that is available" and thus deserving of inclusion in introductory science
classes.
Ewens and Wilf (2010).rebutting creationist silliness is a legitimate activity, for the purposes of educating the
public and the broader academic community. It in no way justifies the inclusion of the rebutted crank ideas in
introductory classes. And, anyway, Ewens and Wilf (2010) didn't actually cite any creationist literature, if I recall
correctly (see the Scott & Matzke 2007 PNAS article for that).
"A practical and rational philosophy of science instruction can be expected to yield the most benefits to society. This
prevents the ossification of didacticism as a rigid induction into what the body of science actually represents."
If students were to be taught scientific topics in proportion to what the scientific community thinks is important, I
would support that; but this, too, would leave no room for fringe and crank pseudoscience.
"The use of informative and appropriate material taken from peer-reviewed journal articles, and where relevant to
the science curriculum, can serve as an educational supplement to that of the traditional textbooks. Journal articles
are where scientific research is announced and these findings are reviewed - it is important for teachers to describe
just how science works. Such an exercise should prove to be acceptable to all parties when it is realized that the everincreasing
understanding of students requires a better method of formal education."
This whole article is just an attempt of Bozorgmehr to continue his one-man campaign against evolution by
harassing various journals until occasionally something gets published. This article is basically mostly about
communicating "nyah, nyah, I got my [deeply-flawed] article published in [insert obscure non-biology journal]' to
NCSE.
As I have shown in this review, the article contains numerous scientific errors, and fails to even attempt to make the
kinds of arguments that would have to be made to make a serious case for including Bozorgmehr's work or similar
work in introductory high school biology classes. Thus there would be no reason for NCSE Reports to publish it,
except with a rebuttal like the above, which would serve as a primer for the sadly inevitable day when Bozorgmehr
or someone similar starts waving around an article like Bozorgmehr's in front of some bewildered school board.
I recall that I think I have seen Bozorgmehr post the rejection reviews he has received from other journals online. I
suppose this is up to the NCSE Reports editor, but I have no objection to this, as long as my review is posted in its
entirety without modification, and my name is attached.
Nicholas J. Matzke
matzke@berkeley.edu
U.C. Berkeley Department of Integrative Biology.

He got his Master's in geography and doesn't understand jack shit about molecular biology beyond the buzz words.

Nick Matzke started the PhD program in Integrative Biology in Fall 2007. He has a double B.S. in Biology and Chemistry from Valparaiso University, and a Master's degree in Geography from U.C. Santa Barbara. Before coming to Cal, he worked for three years as a Public Information Project Director at Oakland-based National Center for Science Education, a nonprofit devoted to defending the teaching of evolution in the public schools

Atheistoclast wrote:I just got a manuscript I submitted to the Reports of the NCSE rejected. The reviewer, none other than Nick Matzke himself, insisted on not remaining anonymous: You can read his review of my work at the following site:

http://talkrational.org/showthread.php?t=47306

Enjoy.

Atheistoclast wrote:He got his Master's in geography and doesn't understand jack shit about molecular biology beyond the buzz words.

Onyx8 wrote:I wonder if you can get a degree in that?

Atheistoclast (on TalkRational) wrote:Nick is hailed by the likes of the NCSE, NAS, ACLU and AAAS as a valiant defender of the theory of evolution. However, I do not consider Matzke as my "peer" since he doesn't conduct research with anything like the rigor that I do.

Atheistoclast wrote:He got his Master's in geography and doesn't understand jack shit about molecular biology beyond the buzz words.

Weaver wrote:He also got his PhD in Integrative Biology.

Forget about that one?

http://ib.berkeley.edu/people/students/ ... person=370

Paul wrote:

Atheistoclast (on TalkRational) wrote:Nick is hailed by the likes of the NCSE, NAS, ACLU and AAAS as a valiant defender of the theory of evolution. However, I do not consider Matzke as my "peer" since he doesn't conduct research with anything like the rigor that I do.

(my bolding above)

laklak wrote:

Onyx8 wrote:I wonder if you can get a degree in that?

Sure. It's called "Christian Theology".

ramseyoptom wrote:I have to admire Clastie's openess in publishing such a critical statement about his papers. However it does seem a very public exercise in self-flagellation, his honesty in displaying the comments of his critics is certainly refreshing in a creationist.