Researching Creation

November 29, 2009

Biological Change / On-the-fly Untemplated Protein Modifications

JB

A HUGE new discovery - it appears that cells can react to cell stresses, and then start building modified proteins to account for the stress.  These modifications are not genetically coded. 

In the specific test case, cells reacted to the presence of reactive oxygen species (ROS) by adding methionines into proteins at various locations to protect the protein's function.  The sulfur in methionine helps protect against ROS in the cell.

Here is the writeup in science daily.

HT to Darwin's God.

November 15, 2009

Discussions around the Web / Tim Heaton on Creationism

JB

Tim Heaton wrote a number of criticisms of young-earth Creationism in a recent paper in the journal Science and Education.  Tim has been kind enough to discuss the paper over at Paul Garner's blog.  He also posted a copy of that paper and one other.

Anyway, it would be worth your while to read the paper, Paul Garner's post, and the comments.

October 24, 2009

General / CleverBadger's Response on Creation Research

JB

CleverBadger made a response to my earlier post

I don't have time to respond at the moment, but thought my readers might appreciate it.  I don't have time at the moment to respond, but if I find time later I will add my response(s) to the comments.

Anyway, many thanks to CleverBadger for taking time to seriously engage on the issue.  If my readers have their own comments (positive or negative) on CleverBadger's arguments, please post them in the comments as well!

October 23, 2009

General / Summer 2009 BSG Newsletter is Available

JB

The new BSG (Creation Biology Study Group) newsletter has now been posted (note - you may have to rename the file to have a .pdf extension after downloading).  If you are a BSG member, you can view all the newsletters on the newsletter page.

If you are not a BSG member, you can sign up here (I believe the membership fee is somewhere around $20).  The BSG is a YEC-oriented biology group (and we ask that you be with us in our general goal), but it does not require any statement of faith to join.

If you would like to contribute to the next newsletter, please email me at bsg@bartlettpublishing.com.  The goals and types of content we are looking for is found in the original announcement of the newsletter.

For more information about the BSG, see the BSG website.

Thanks to all of those who contributed articles for making this a great newsletter!

October 12, 2009

Discussions around the Web / Is Creation Research Just Circular Reasoning?

JB

One objection that I often hear about Creation Research and specifically Creation-oriented journals is the accusation of "circular reasoning".  A recent discussion I was having with Clever Badger was on just this topic.  While I don't think that the charge is legitimate, I believe that those who level the charge are doing so in good faith.  There is a legitimate question on the methods of science in there, and I think it deserves a good and well-thought-out answer.

Here is Clever Badger's objection:

The problem here is that it presupposes a literal interpretation of Genesis. In other words, the ARJ [Answers Research Journal] isn’t looking for objective research – it’s looking for writers who can force data to fit a predetermined conclusion (e.g. that the diversity of life on Earth today can be somehow traced back to pairs of animals coming off of a boat several thousand years ago). That’s not how science works. The ARJ is basically saying that they don’t want articles that disagree with their position

Basically the accusation is circular reasoning - that people are presupposing a literal interpretation of Genesis and then using that presupposition to argue for that very conclusion, and call it a publicly valid argument.  I have, indeed, seen bad arguments of that sort, but I think that Clever Badger is misinterpreting a lot of what is going on - both in Creation circles and secular circles.

First of all, Clever Badger is implicitly stating that the same kind of presuppositions are not occuring in secular science.  To examine that claim, let's take a look at two journal purpose statements.

The first, is the Creationist ARJ's journal (note that while I am a fan of ARJ, the reason that they are being focused on is merely because AiG [the publisher of ARJ] was the original target of Clever Badger's post - there are many other good Creation journals as well):

ARJ is a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework...

ARJ is a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework...

Now, let's look at the mission statement for another publication - the journal Evolution:

Evolution, published for the Society for the Study of Evolution, is the premier publication devoted to the study of organic evolution and the integration of the various fields of science concerned with evolution. The journal presents significant and original results that extend our understanding of evolutionary phenomena and processes.

So, ARJ is a journal published by a Creation organization, for the purposes of furthering our understanding of Creation in an interdisciplinary manner.  Evolution, is a journal published by the Society for the Study of Evolution, for the purposes of furthering our understanding of evolution in an interdisciplinary manner.

Hmmmm......

As you can see, every scientist presupposes the basic tenets of their field.  The purpose of these fields is to learn and understand more on the basis of these tenets.  The journal Evolution presupposes common ancestry (I challenge anyone to find an article in Evolution giving a comparison of common ancestry to other hypotheses), the journal ARJ presupposes Biblical Creation. 

I think that the stumbling point is that many people think that Biblical Creation is the stopping point, rather than the starting point.  For some people it is, but for many Creation researches, Biblical Creation is the starting point of what we do.  The goal is to use Biblical Creation to better understand nature.  In fact, many of the foundational principles of many branches of science were based on just that supposition.

For instance, many do not know that Steno, known as the "Father of Geology", was motivated by Creation, and used Biblical Creation principles to formulate his laws of stratigraphy.  It was precisely because he believed in the global flood that gave him the intellectual capacity to argue that Shark's teeth found inland were the remains of buried animals and not created by God in situ, as was a common geological notion in his time.

Likewise, Gregor Mendel, was motivated by his disbelief in evolutionary principles for his experimentation in pea plants.  His paper, which is the foundation of genetics, was actually explicitly anti-evolutionary (it took the evolutionists about 50 years to find a way to incorporate genetics into evolutionary theory).

Similar stories exist for Keppler and many other scientists who were foundational to their field.  They used Scripture to understand Creation better. 

Another interesting example is the Big Bang theory.  Most people don't know that LeMaitre, who originally proposed the Big Bang, was working from the same data everyone else was.  The only difference is that he also added to his data a touch of Biblical history and Catholic theology.  The notion that the universe expanding was not new, but LeMaitre was the one - based on his belief in a beginning - who used that notion to propose that the world originated as a "cosmic egg" (which is very Thomistic in its outlook).  In fact, an early, unpublished paper by LeMaitre described the his ideas specifically in support of Genesis, saying that the beginning happened "as Genesis suggested it".

As you can see, presuppositions are present in all of science, and Biblical presuppositions have been key in the founding of nearly every major branch of science.  Many people have a view of science that is very dry, calculating, and objective.  Science has never been as dull, or as objective, as people's descriptions of it.

In specific reference to Creationism, it is interesting to note that criticisms of evolution have been allowed in the secular, scientific literature, but only when it is posed as an "unsolved problem" for understanding evolution, rather than as a possibility that evolution is false.  For instance see this abstract.  I know of several ID papers published in this same manner over the last few years, but the authors have asked me not to disclose them as IDists because they want the papers to be evaluated "on their own merits".

So, going back to my discussion with Clever Badger, Clever Badger also notes the apologetic aspect of Creationism.  However, showing that scientific theory X doesn't make sense, or that theory Y is a better explanation for facts A, B, and C is in fact a legitimate part of science. 

But can an external belief be valid in such a context?  Absolutely so!  External beliefs are perfectly valid heuristics for finding scientific ideas.  In fact, in Gilkey's Creationism on Trial, he notes that historians of science believe that Gould's punctuated equilibrium came from his Marxist beliefs (they both hinge on revolution, rather than gradualism, being the defining mode of life).  Why isn't this invalid?  Because Gould never uses Marxist ideology as evidence.  The submitted evidence is all externally verifiable.  Likewise, for apologetic Creationism, the Bible is used as a heuristic for finding one's own position, but not as an external justification for it.

So, to summarize, there are two basic forms of Creation research (though many engage in both):

a) use Biblical Creation as an assumption to learn more about nature.  This is not circular because it does not use the findings as a reason to believe that Biblical Creation is true, nor does it claim that its findings should be reasonable or valid to people in a different perspective.

b) engage in apologetics for Biblical Creation.  This is not circular because although the Bible was used by the researchers as a heuristic for their own positions, it was not used as an external justification to others.

Certainly there is interplay between these two poles, as some ideas discovered by the group in (a) can in fact be used and/or proven without reference to scripture, despite the fact that it was originally studied in that way.  Likewise, apologetics can sometimes reveal very interesting aspects about the nature of creation.  This latter notion is often what happens with my studies.  It starts off as apologetic, but later sparks additional ideas and questions which lead to a greater understanding of God's creation for those who share my assumptions.

So, hopefully this gives you a little insight into the thinking behind Creationism.

October 11, 2009

Biological Change / Dried Green Tomatoes, Coordinated Mutations, and Natural Evil

JB

I've been on quite a gardening kick lately, and one of the things I have been growing is tomatoes.  I am growing several different heirloom tomatoes, and none of them want to ripen on the vine.  Either that, or being ripe on the vine is what is attracting all the bunnies to eat them.  In any case, I have to pick them while they are still green.

Well, my last two batches of tomatoes decided that they didn't want to ripen up.  They just wanted to stay green.  Now, I know that Fried Green Tomatoes is a classic southern dish, but that just takes too much work and is too much of a mess.  So, I decided to try drying them.  I just sliced them up, stuck them on a rack with a little salt, and stuck them in the oven @ 225°F for a few hours.  They tasted delicious. There's only one problem - many people think that green tomatoes are poisonous.

This is because they are part of the Solanum genus (nightshades).  Solanums have a type of chemical in them called alkaloids, the most famous of which is probably Solanine.  This substance is neurotoxic to humans.  Many people say that green tomatoes shouldn't be eaten in medium or large quantities because of the large amounts of solanine in them (but ripe, red tomatoes are fine because the solanine gets catabolized during ripening).

So, curious as to whether I was creating a toxic hazard or an edible treat, I decided to do some digging.  What I found was that

  1. Most reports of green tomatoes being toxic are entirely based on their being part of Solanum and therefore containing solanine, not on any real case reports of someone getting sick (nearly all examples of someone getting sick that I read about were from potatoes [not tomatoes] that had turned green)
  2. Technically, in tomatoes, it isn't even solanine, but rather a related compound called tomatine, which is produced.
  3. There has been no reports of tomatine causing illnesses, and some reports on tomatine's beneficial properties (including reducing cholesterol)
  4. You may even be able to eat the leaves of tomato plants safely
  5. Peruvians eat a variety of red tomatoe which has the same tomatine content as green tomatoes, without any apparent ill effects

So, I'm not as worried as I was about my dried green tomatoes, but I'm still not completely convinced they are safe.  If anyone knows anything more, please post in the comments.

But that's not the interesting part.

While I was investigating, I cam across this paper on tomato alkaloids.  On page 5759 (the 9th page of the PDF) it gives this amazingly interesting fact:

Until the recent discovery of dehydrotomatine, it was
thought that tomatoes contain only one glycoalkaloid, usually
called α-tomatine or tomatine. The question arises why each
of the major Solanum plants produced two glycoalkaloids
[potatoes, α-chaconine and α-solanine (106); eggplants, solamargine
and solasonine (115); tomatoes, dehydrotomatine and
α-tomatine].

So to my mind, this brings up several interesting questions:

  1. Why are these glycoalkaloids in pairs?
  2. More importantly, if we assume that these are from an original created kind, how did each one manage to get a different type of glycoalkaloid, and still get exactly two?
  3. Is the usefulness or harmfulness of these substances an intentional part of creation or simply a byproduct of its diversification method?

So, for instance, many of these substances are used medicinally.  Is the wide variety of alkaloids there for the purpose of healing, or is that merely something that we've imposed on them?  Are the ones that are toxic there for the purpose of harming humans, or is that just a byproduct of how the plant's biochemistry evolved?

The wierd thing, which I think may be key to figuring at least some of this out, is that these alkaloids are evolving in pairs.  I think there must be some underlying mutational mechanism which is causing the coordination of the glycoalkaloids.  Thus, with a single mechanism, perhaps both compounds can be changed in a coordinated style, to maintain their synergistic reactions (whatever they are), but yet be modified in a way that is useful either to the plant or to others.  Perhaps the radiation of glycoalkaloids is stochastic - if it were purely stochastic, then this would possibly give weight to the idea that they were _designed_ for medicinal uses, since this would make sure that all (or nearly all) of the potential glycoalkaloids were available somewhere in creation.  If, instead, they were adaptive, then we would probably say that their use to humans is a byproduct and not their reason for existence.

In any case, if I had time, looking into these chemical structures, their gene sequences, and possible mutational mechanisms would make a fun project.  Of course, I may need to wait until the Tomato Genome Project is completed.

I had better stop now and get my last batch of dried green tomatoes out of the oven!

References:

 

October 10, 2009

Biological Change / The Origin of Retroviruses

Endogenous, Exogenous, or Neither?

JB

ARJ has an interesting review paper by Liu and Soper on the origin of retroviruses.  Liu has written a number of papers on retroviruses, and this is in large part a culmination of his work.

The paper has a lot of interesting information:

  • Many retroviral env proteins are immunosuppressant
  • Many retroviral env proteins help cells fuse together to form larger complexes
  • Ty elements in yeast are similar to retroviruses, but lack evn proteins
  • Solo LTR's can be created by an LTR being inserted during the repair of a double-stranded break (indicating that a solo LTR is not necessarily the result of a ERV deletion)
  • Viruses can package pieces of host DNA and move it between hosts (known as transduction)
  • Expressed ERVs prevent infection from similar ERVs
  • Different retroviruses have different target site preferences

The authors use these and other items to infer that retroviruses were originally part of the genome itself, and were later exogenized into free particles for infection.  They also propose that retroviruses were used for horizontally transferring genetic material.

My personal hunch is that retroviruses have neither an origination outside the organism nor inside the originally-created DNA (at least not exclusively).  I tend to go with Blanden and Steele's suggestion in Lamarck's Signature that they are instead used for somatic selection.  That is, somatic cells do the real evolutionary work, and retroviruses package up that material and transport it - either back to the germ line or to other somatic cells. 

Thus, retroviruses are essentially created by (or at least used by) somatic cells to move new genes back to the germ line for more efficient adaptation to new environments.

Anyway, it's a hunch.

October 06, 2009

General / Laps for Little Ones

JB

Support the Little Light House by sponsoring us in Laps for Little Ones

The Little Light House is one of the best ministries I've ever been involved with.  They are a Christian, private, tuition-free school for special-needs kids.  That's right, the kids who go there don't have to pay anything at all.

This isn't day-care - it's an intensive, customized program for each child.  The school day lets out at 1PM, and the staff spends the rest of the day planning each child's next day.  When a child gets to school, they have a card of things that they are going to work on that day.  It's both extremely fun and extremely helpful for the children -- and the parents.

While our oldest son, Danny, was alive, he attended the Little Light House.  His world expanded so much while he was there.  His ability to play with others and interact and do new things hinged upon the teachers at the Little Light House and their love and their help.  Danny had to be fed through a tube, received many, many, many medications at specially-timed intervals, and, if everyone was lucky, he only threw up three times a day.  Yet the Little Light House had no problems seeing to his every need while he was there, and providing every manner of therapy.  At the Little Light House, they have physical therapy, speech therapy, occupational therapy, and probably a lot of other therapies I'm not so familiar with.  And everything is done in a specifically Christian way.

Isaac had the same genetic defect that Danny had, and, had he lived long enough, would have enjoyed the services of the Little Light House as well.  As soon as we discovered his condition, we reserved him a spot there, because we knew that their help was the difference between night and day for us.

Below are pictures of Danny learning at the Little Light House.  Also, for those of you who didn't get to know Danny or Isaac, I pasted their memorial videos below.  In any case, please consider helping out the Little Light House - they have been a huge blessing to us, and to many, many, many other children.

You can donate now by going here.

Here is Danny's Memorial Video:

Isaac's Memorial Video:

A few pictures of Danny at the Little Light House if you don't have time for the video:

The picture below might look like playtime to you, but this was actually crucial for Danny.  He had problems touching a variety of surfaces - many different textures made him cry and gag and puke (yes, really).  The Little Light House worked with him to help him adjust his senses to be able to touch and play with a huge variety of textures.

September 28, 2009

Discussions around the Web / Petrified Logjams, Microbes, Stone tools, and More

JB

Interesting Bits from Around the Web:

September 16, 2009

General / Stone Age Tom-Toms

JB

It turns out that stone-age people developed navigation systems, too.  Here is a report of a system used in England using regularly-spaced markers.

On the amusing side, here are some of the pitfalls that can happen when you try to correct a major finding in a scientific journal.  The take-home lesson - scientists and journal editors are people, too, and science and scientific journals are subject to the same people problems and groupthink that plague every other organization.