How scientists resolve conflicting theories: Origins of Leishmania found

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People have very different opinions about the world. I don’t like melted cheese, but you may love the creamy goodness. Similar scientists develop contrasting hypotheses; however, they base these hypotheses on evidence. How do scientists develop different hypotheses? One scientist may see a pattern in one phenomena and try to apply it to another one to possibly explain why it happens. If two scientists tried to apply different patterns they observed to the same problem, they would end up with different opinions. A reason specific to phylogenetics that scientists have different hypotheses is because of morphology. Morphology is the study of form and structure of organisms. Before DNA became widely used, the only way to figure out how species were related was to look at their morphology and the fossil record. From there, similar looking species would be put in the same groups. One could hypothesize that bats and birds are closely related because they both can fly, but another may hypothesize that they are distantly related because bats nurse their babies with milk and birds do not. Molecular phylogenetics is one way that scientists can have more evidence to understand relationships among species because DNA is the hereditary material and not subjective to different opinions like morphology. An example of the utilization of DNA is the resolution of the debate between scientists about where the parasites that cause leishmaniasis originated.

Welcome to the New Panda’s Thumb

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Skadoosh
Skadoosh!

We apologize for the outages that PT has faced over the last few months. Our server has been dying, and it has taken a bit of effort to migrate to a new one.

In the process, we have redesigned both our website and the our backend experience, which took a lot of migration of content. Here are the things you will notice:

  • Smoother, modern feeling layout
  • Support for mobile devices
  • Comments powered by Disqus

The new site is still a work in progress, and here is what we will will implement in the coming months

  • Search functionality
  • The Bathroom Wall
  • RSS Feed
  • Migration of old comments to Disqus
  • Clean up of old posts which did not convert well to the new system
  • More content

Please let us know how we are doing in the comments.

Creationist classification of theropods

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Kane_Figure_1.jpg
“Liaoning scene” by Emily Willoughby.

Guest post by Jonathan Kane. Mr. Kane describes himself as an “armchair paleontologist” who worked as an intern at the New Jersey State Museum under natural-history curator David C. Parris from 2001 to 2005. He is the lead author of God’s Word or Human Reason? An Inside Perspective on Creationism , coauthored by Emily Willoughby and T. Michael Keesey, shortly to be published by Inkwater Press.

A major focus of the upcoming book is the fossil evidence for a relationship between theropod dinosaurs and birds. However, the book did not have the space to address how coelurosaurian theropods are classified by creationists in as much detail as he would have liked. He has therefore prepared a separate article for The Panda’s Thumb on how creationists classify these animals. Although it can be read as a stand-alone article, he thinks it is best appreciated as a supplement to his forthcoming book.

Relations between species

Modern young-Earth creationists almost universally accept that speciation is possible. This image from the Creation Museum shows how, from the creationist perspective, all dogs, wolves, foxes, and coyotes share a common ancestor and are descended from a single pair of canids that were on Noah’s Ark. In contrast to the “tree of life” referred to by supporters of common descent, creationists sometimes refer to the “orchard of life,” made up of many separate trees. Each of these trees represents a group of interrelated species, which is unrelated to other such groups, as shown in this chart used by Ken Ham during his debate with Bill Nye.

From the creationist perspective, each of these separate trees is known as a created kind or baramin, from the Hebrew words bara (create) and min (kind). Species within a baramin usually are considered to share a common ancestor, although not always. Any currently living baramin of land animals would be descended from a pair of individuals that were aboard the Ark, but baramins of sea animals or plants would not necessarily have gone through that population bottleneck. For plants and marine animals, each baramin could possibly contain multiple lineages that have been separate ever since they were created. (Ken Ham’s image does not clearly show this possibility, but it’s described in this creationist technical paper, using the baramin of grasses as an example.)

One of the tenets of this view is that while species within a baramin may be related to one another, they cannot be related to any species outside the baramin. Therefore, in any case where a species combines anatomical traits from multiple baramins, the creationist perspective requires it to be placed firmly in one baramin or the other. Placing it often is no easy task. This article from Talk.Origins summarizes how creationists have attempted to classify several fossils of hominids that have a combination of ape-like and human-like anatomy, based on the requirement that every fossil must be classified as either fully human or fully ape. Opinions have ranged from classifying them all as apes (Jack Cuozzo) to classifying them all as humans (Peter Line), with many other viewpoints in between.

How then are dinosaurs and birds classified? Like apes and humans, creationists almost universally consider coelurosaurian theropods and birds to be separate baramins. Unlike in the case of apes and humans, though, they have generally not attempted to come up with complete classification systems to identify the division between birdlike dinosaurs and birds. (There are a few important exceptions, which I’ll discuss later on, where creationists have attempted to identify the division.) However, Answers in Genesis has done the next best thing. Whenever a new specimen of birdlike dinosaur is discovered, they have typically published an article explaining which way they classify it.

False promise of genetically modified crops

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The Times is more polite than I am; today it ran an article Doubts about the promised bounty of genetically modified crops, by Danny Hakim. Well, I read the article and looked more closely at the supporting material, Broken promises of genetically modified crops, by Karl Russell and Danny Hakim, and I frankly have no doubts. As Mr. Hakim writes,

An analysis by The Times using United Nations data showed that the United States and Canada have gained no discernible advantage in yields — food per acre — when measured against Western Europe, a region with comparably modernized agricultural producers like France and Germany. Also, a recent National Academy of Sciences report found that “there was little evidence” that the introduction of genetically modified crops in the United States had led to yield gains beyond those seen in conventional crops.

At the same time, herbicide use has increased in the United States, even as major crops like corn, soybeans and cotton have been converted to modified varieties. And the United States has fallen behind Europe’s biggest producer, France, in reducing the overall use of pesticides, which includes both herbicides and insecticides.

In addition, Mr. Hakim notes that

the use of toxins that kill insects and fungi has fallen by a third, but the spraying of herbicides, which are used in much higher volumes, has risen by 21 percent.

By contrast, in France, use of insecticides and fungicides has fallen by a far greater percentage — 65 percent — and herbicide use has decreased as well, by 36 percent.

Monsanto said in a statement,

While overall herbicide use may be increasing in some areas where farmers are following best practices to manage emerging weed issues, farmers in other areas with different circumstances may have decreased or maintained their herbicide usage [my italics].

Or they may have increased or maintained their herbicide usage.

One of the striking features in the supporting information, which is all graphical, is the graph of “Sugar beet crop yield.” Sugar beet yield increased markedly more in Western Europe, where GMO’s are not used, than in the United States. Perhaps more strikingly, the graph shows not the slightest hint of an increase in yield in the United States after GMO’s were introduced.

I am by no means an expert, and i do not mind if they want to genetically modify a tomato so that it will grow in a desert. But I have always been suspicious of GMO’s such as Roundup Ready corn, largely because of the problem of resistant pests evolving, and indeed Mr. Hakim notes,

Growing resistance to Roundup is reviving old, and contentious, chemicals. One is 2,4-D, an ingredient in Agent Orange, [whose] potential risks have long divided scientists and have alarmed advocacy groups.

Despite the gratuitous reference to Agent Orange, Mr. Hakim’s article is mostly dispassionate and very thorough, and I suggest you read it for yourself, and also look closely at the supporting information.