Per Request: How do bones regenerate?

I got a request to write a post on how bones regrow or grow for the first time, so here goes:

There are 3 different types of cells in bone.  Osteoblasts are responsible for making and putting down new bone, osteoclasts are responsible for taking up and getting rid of old bone, and osteocytes are osteoblasts that have been trapped inside the new bone and then work to maintain the bone after it has been constructed.  So, here’s what happens:

The osteoclasts drill through bone tissue to clean it out, and then osteoblasts follow behind depositing new bone tissue on the sides of the inside of the bone, creating this new tissue that surrounds either a blood vessel or a nerve.  When a bone is broken, the first thing osteoblasts lay down is what’s called “woven fiber” bone tissue; this tissue is much faster to create and lay down (providing quick structure) but is not as strong.  Later, because it takes more time, osteoblasts replace that woven fiber tissue with “lamellar” bone tissue, which is nicely organized in sheets that is very strong. 

So, a sensible follow up question would be: how does bone grow?  A bone begins as cartilage and then layers of bone begin to develop around it while cells destroy and take up the old cartilage.  Then, cells begin to move to the ends of the bone towards the “active growth centers,” where they stretch out the bones.  After the bone has finished growing, the cells mineralize the bone to make it tough and strong.  When a bone mineralizes, it ceases to grow forever.  So, when humans stop growing, that is because all of our bone has been mineralized.

Comment if there are any questions, but that explains the basics about how bone tissue can regenerate and how bones can be fixed.

Combating Data Manipulation I: Common Mistakes in Data Presentation

The first part of combating data manipulation is recognizing when a graph or chart or data set is misleading in some way.

(1) To understand the first way this can happen, we need to understand “what is measurable”?  Something that is measurable has a unit (e.g. length can be measured in inches, weight in grams, etc.).  Many advertisements and commercials make use of numbers and measurements that functionally mean nothing, because they are numbers with no units.

http://2.bp.blogspot.com/_og7k0zkwKHk/TT7P3HR3YgI/AAAAAAAAAgQ/Z0fXBFYoaSI/s1600/Angelica+Panganiban+Pantene+Ad.jpg

So Pantene promises two times more shine in hair; how is shine measured?  What does that mean?  This number “two times” does not mean anything, but it sounds much more persuasive than saying “you’ll get some more shine in your hair.”

(\http://brianar92.edublogs.org/files/2010/09/maskk1.jpg)

Here is another example.  Maybelline promises a 65% lift to the eyelashes, but how do we measure lift in eyelashes?  This is persuasive, but definitely not meaningful.

These numbers with no meaning are purely used for persuasion and the first, and probably the easiest, use of numerical manipulation that we can spot.

(2) The second way people manipulate data to persuade is known as “cherry-picking.”  This is when certain data is presented, but other data that does not support the point is ignored.  Charles Seife in Proofiness presents an example in George Bush’s descriptions of the apparent success of the No Child Left Behind Policy.  He claimed that students were in general improving their test scores, ignoring data from 12th grade students whose test scores actually decreased.  Secondly, those scores that did increase have actually been increasing slowly for decades, way before the passage of the legislation.  Bush cherry-picked data that supported his point and his policy.

(3) The third way is comparing data that should not be compared (e.g. comparing data from different years when the conditions were very different).  Seife uses the example of the Blue Dog Coalition criticizing the Bush Administration for borrowing a lot of money from foreign nations.  They claimed, “Throughout the first 224 years (1776-2000) of our nation’s history, 42 U.S. presidents borrowed a combined $1.01 trillion from foreign governments and financial institutions according to the U.S. Treasury Department. In the past four years alone (2001-2005), the Bush Administration has borrowed a staggering $1.05 trillion.”  While the comparison of numbers sounds incredibly convincing, if you think about it, the value of the dollar in 1776 was vastly different than the value of the dollar today or in 2005, and therefore this comparison does not make a whole lot of sense.  This is a common problem with the comparison of test scores from different years; Michael Winerip in The New York Times describes the mayor of New York boasting about the increase in test scores for fourth graders, when many of the educators actually admit that the test just got easier.  Therefore, the comparison across years is inaccurate.

(4) Finally, the last type of data manipulation is just changing the graph itself.  If one axis of the graph represents only 0-1 (of whatever unit the graph is displaying), it would look vastly different than if the axis went from 0-10 or 0-50.  Making sure that the axes and type of graph accurately display the data is extremely important.

Up Next: an in-depth discussion of error (especially as it relates to polls and voting)!

Works Cited

Charles Seife, Proofiness

http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=132×3162826

Combating Data Manipulation: Introduction

After reading a few books on data presentation and statistics and probability theory, I have decided to create a 10-post series about things everyone should know about data.  As Charles Seife mentions in the first few paragraphs of his book Proofiness, putting numbers to an opinion or thought tend to make people believe the opinion more than without that mathematical or numerical backing.  Seife, in his introduction, uses Joe McCarthy as an example of this: when he declared that the State Department harbored communists, his argument got even more persuasive when he declared that he could name 205 of them.  Afterwards, that number fluctuated from 207 to 57 to 81 to even less than those, but what mattered was that McCarthy had a number to back his statement up.

Sooner or later, everyone will encounter some data set, graph, chart, or statistic that is either made up entirely or somehow false.  Unfortunately, a lot of people end up basing opinions or votes on these mathematical falsehoods simply because the skills of identifying data manipulation are not widely taught.

These posts will have applications in statistics, economics, political science, as well as many other fields, approached from a mathematical and statistical perspective.  And, while I will be using books such as Seife’s Proofiness and Leonard Mlodinow’s book The Drunkard’s Walk: How Randomness Rules Our Lives, I will verify that the information I post here is as accurate as I can make it.

Works Cited:

Charles Seife, Proofiness

Leonard Mlodinow, The Drunkard’s Walk: How Randomness Rules Our Lives

Organic Foods: The Definition

Are organic foods better for you than non organic foods?  Are non organic foods dangerous because they use pesticides and herbicides?  The answer to these questions lies, in some part, in the definition of organic farming.

The definition is, surprisingly enough, extremely loose.  “Organic foods” does NOT mean that pesticides or fertilizers were not used.  Organic farming cannot use synthetic pesticides or fertilizers and it cannot use genetically modified organisms (for more information, see the GMO’s page).  While this may seem like organic foods are safer because synthetic pesticides can be dangerous, this is not necessarily the case.  To put it in perspective, arsenic and cyanide would be “natural” pesticides, and therefore allowed under the definition of organic farming.  While there are certain exceptions in the organic farming definition (which include banning arsenic and cyanide), there are equally poisonous chemicals that are completely natural and therefore allowed under organic farming, but should definitely not be ingested by humans (such as hydrogen peroxide).

So, the bottom line: just because something is organic does not mean that pesticides and dangerous chemicals were not used.

More in-depth posts on the benefits and disadvantages of organic foods to come!

 

http://www.epa.gov/agriculture/torg.html#National%20Organic%20Standards

http://www.epa.gov/agriculture/torg.html#National%20Organic%20Standards

http://www.ams.usda.gov/AMSv1.0/NOPPetitionedSubstancesDatabase

http://www.ecfr.gov/cgi-bin/text-idx?c=ecfr&sid=6f623e1de5457587ccdfec12bc34ed1c&rgn=div5&view=text&node=7:3.1.1.9.32&idno=7#7:3.1.1.9.32.7.354

GMO’s: Why is there a debate?

I recently stumbled across a few Scientific American articles (links below if you want to read the whole articles – I recommend it, they are really interesting) and thought I’d share some more information about GMO’s.

There was a study that said GMO’s can cause tumors?

In the journal Food and Chemical Toxicology, a paper was published two years ago that concluded that genetically modified corn caused brain tumors in the rats that they studied.  I have heard many people who oppose GMO’s cite this article as proof that genetically modified food can be dangerous.  Recently, the journal retracted that paper, because the paper claimed these huge conclusions off of a study with a very small sample size, meaning they studied only a few rats.  In a scientific study, smaller sample sizes decreases the chances that a definitive conclusion can be reached, because other factors are more likely to affect the experiment with a small number of rats than a large amount.  Therefore, the journal decided the paper claimed too many conclusions that the evidence did not support.

The second article I have cited also lists (in 3-4) many other research papers claiming GMO’s are dangerous, in which the conclusions of these papers have been overstated by the media. 

Mixing genes from different species is unnatural

Actually, a human genome can consist of DNA sequences that are nonhuman; viruses can transmit DNA from one species to another easily, and they have been doing this for millions of years. 

But the plants contain pesticides that we would eat

Many of those herbicides and pesticides are harmful to insects and plants, but not harmful to humans.  Many of the genes that are inserted into plants are from bacteria that we use in organic farming anyways as natural pesticides and herbicides; the only difference is inserting that gene into plants rather than using the bacteria or organism that the gene originated from. Therefore, we end up consuming these anyways.

 

Testing of GMO crops should definitely continue, but so far no conclusive evidence has been shown that all genetically modified crops in general are dangerous.

http://www.scientificamerican.com/article/study-linking-genetically-modified-corn-to-cancer/

http://www.scientificamerican.com/article/the-truth-about-genetically-modified-food/?page=5

Evolution

I have been recently thinking about the misinformation that abounds when it comes to more complex biological topics such as evolution, and therefore I decided that this was a reasonable time to post the basics of evolution and the biggest misconceptions.

What is evolution?

Evolution, as defined by Zimmer and Emlen 2012, is “the change in proportions of heritable properties of groups of organisms over the course of generations.”

This is a fairly technical definition, as most biological definitions are.  First of all, the phrase “change in proportions of heritable properties” essentially means that there has been a change in the amount of a certain trait in a population (I’ll get to explaining how this change happens in a bit).  The key word in that phrase, however, is “heritable.”  For evolution to happen, the trait in question needs to be able to be passed down from one generation to the other, otherwise the specific trait cannot spread to the next generation and evolution would never occur.  The second part of the phrase, “groups of organisms over the course of generations,” means that evolution happens in a population, not an individual, and it happens over at least one generation.  So, if we put this all together, we get that evolution is the change in the amount of a given trait from a parent generation to an offspring generation.

What causes this change?

This is what we refer to as the “Four Forces of Evolution.”

(1) Mutation: mutation is solely responsible for generating all of the diversity we have on this planet.  A mutation is simply an alteration in the DNA when it replicates.  For example, in a germ cell (that is, a sperm or an egg cell), when the DNA from the parent replicates, sometimes the enzymes and proteins that are replicating the DNA make mistakes.  These mistakes can be small, such as switching out one nucleotide (defined in the previous post on GMO’s) for another, also known as a point mutation, or they can be very big, such as reversing an entire segment of DNA.  However, even the smallest mutations can cause huge changes in the offspring.  So, the DNA has been mutated by a mistake in the replication and that mutated DNA is then passed onto the offspring.  Therefore, the offspring has a different trait than the parent.  This alone can be considered evolution!  There has been a change in the amount of a certain trait (a new trait has been introduced to a population) from the parent generation to the offspring generation.  However, mutation ONLY creates diversity; mutation cannot spread this new trait or make it more favorable.  Mutation just introduces new genetics to a population.  The other three Forces of Evolution are responsible for causing this trait to spread, generating more of a difference in the amount of the trait, and therefore generating more evolution!

(2) Gene Flow: Gene flow simply refers to new genes being introduced into a population because of immigration or genes leaving a population due to emigration.  If new individuals of the same species, but from a different population and therefore with different genetics, enters a population and begins breeding with that population, it could cause a change in the amount of certain traits, especially an increase in the traits that that individual brought.

(3) Genetic Drift: This is arguably the most complicated to understand.  Genetic drift simply refers to random variation.  For example, if a few males have a certain trait but, for some reason, none of them mate and pass on their genes, then that trait will be significantly less in the next generation.

(4) (Natural) Selection: This is the most commonly known when discussing evolution, but is actually only one of the four Forces of Evolution.  Gene Flow, Genetic Drift , and (Natural) Selection all work to spread certain traits in a population or reduce the amount of a certain trait in a population.  (Natural) selection refers to when some individuals reproduce more than others because of their traits.  For example, if there is a population of shellfish with two different colored shells, one that stands out against the sand and one that blends into the sand, the individuals with a shell that stands out are more likely to get eaten.  Therefore, they don’t get to pass on their genes for the shell that stands out to the next generation, and therefore in the offspring generation the amount of shells that stand out are much less.  This is a change in the amount of a trait across generations, and therefore it is evolution.  I have been putting the word “natural” in parenthesis when talking about selection because biologists today tend to just use the phrase selection, as the “natural” does not add much anymore.

Additionally, I would like to emphasize that evolution is NOT directed and has no conscious thoughts.  Evolution does not decide to keep one trait or another, the trait is kept in a population due to either gene flow, genetic drift, or selection.

Now, hopefully, you have a better understanding of the definition of evolution and why a trait MUST be heritable to evolve (because it has to be passed down to another generation) and why evolution cannot occur in an individual (because any changes in an individual will not be passed down to another generation).

Arguments Against Evolution and Misconceptions About Evolution

(1) Evolution has never been observed: This is not true; evolutionary biologists have, in fact, traced differences between generations of certain populations of organisms.  In fact, an experiment performed by Buri in 1956 demonstrated that evolution does occur (he studied evolution by genetic drift).  He set up 100 vials with flies that are heterozygous (this means that they have two different types of the gene for eye color: they have one for red eyes and one for white eyes; this manifests itself as orange eyes for these flies).  Buri let them mate and reproduce, every generation randomly selecting 8 males and 8 females to reproduce.  At the end of the experiment, 25 vials had flies with all red eyes, 25 vials had flies with all white eyes, and 50 vials had different proportions of flies with red, white, and orange.  This in itself is evolution in progress.

(2) Evolution is only a theory: The idea of a scientific theory is very, very different from the colloquial use of the word theory.  In every other context, theory means something that has only been thought about, but not put into practice.  In science, a theory is an idea that has been rigorously tested by experimentation and shown to be true, but not proved (because nothing in science can ever be proved, not because science is not a good way to discover knowledge, but just because all scientists are naturally skeptical).  To put it in perspective, gravity is also a theory.  As is the idea of germs.

(3) How did life begin if all life evolved from other life?  To answer this, I’d like to direct you to the first picture I posted in the “Rationale” post.  Number 7: “Thou shall not argue that because of our ignorance, claim must be true or false (Ad ignorantum).”  Just because scientists do not have an answer for everything, including the ever evasive question of how life began, does not mean that everything about science is false or that everything about that particular idea is false.  It just means science is a continuous process.

(4) There are gaps in the fossil record: This is true, and there will always be gaps in the fossil record because we will never get fossils of every single type of creature.  However, that does not mean that the fossil record is incomprehensible.  We have enough data on primitive organisms, as well as observations of primitive, living organisms (also known as living fossils) to determine extreme similarities between organisms from millions of years ago and today.  We can now also use techniques such as molecular and genetic data.

(5) The Second Law of Thermodynamics says evolution is false: The 2nd Law of Thermodynamics is very often misinterpreted.  It says that the entropy of an isolated system is constant or increasing.  Entropy is a measure of disorder and heat, and so many people take that to mean that if disorder is always increasing, then how can something more ordered come from nothing?  Well, the 2nd Law of Thermodynamics discusses an isolated system, which means no energy or matter is flowing in and out of the system.  This is definitely not true for Earth and for life; energy and matter are constantly flowing in and out of Earth from space and flowing in and out of habitats.

(6) There are no transitional fossils: This means that there are no fossils found in the midst of evolution.  First, from what we now know about evolution, we can tell that since an individual does not evolve, we will not find a fossil that is right in the middle of becoming one organism from another.  However, if this argument is trying to say that we haven’t found an organism that links two different species together (an organism in the middle of a lineage), that’s just not true.  We have found fossils of species that we can identify having certain traits of more primitive organisms, but lacking traits of more modern organisms.  We have also found fossils of species that have similar traits to organisms we see today.

The most important thing to keep in mind when it comes to evolution is Number 7 in the Commandments of Logic: just because we don’t know something yet does not mean that the entire theory is false; it just means that scientists are still discovering things.  If you have any questions, feel free to comment!

http://www.talkorigins.org/faqs/faq-misconceptions.html

http://rationalwiki.org/wiki/Second_law_of_thermodynamics

http://www.bestbiblescience.org/top.htm

http://www.icr.org/home/resources/resources_tracts_scientificcaseagainstevolution/

GMO’s

What is genetic modification/genetically modified organisms (GMOs)?

Genetic modification is an alteration in the DNA sequence or the genes of any organism (including animals, plants, and bacteria).  All organisms have genetic material, either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid).  DNA and RNA are made up of repeating structures called nucleotides, and DNA and RNA make up genes.  These genes “code” for different traits, which can be physical, behavioral, etc.  Genetic modification changes that DNA in some way to produce a desired trait.  They do this in a few ways; one way uses a “gene gun,” which inserts a gene into a sequence.  Another uses viruses that are created to go into a cell and inject genetically modified DNA instead of their viral RNA.

What is the controversy?

While genetic modification has been used widely in bacteria and even some animals for laboratory experiments, the controversy comes from the use of GMO’s in agriculture.  For example, the common complaint is against Monsanto, a large corporation who patented “RoundUp,” an herbicide that is meant as a weedkiller.  Then, they modified and sold plants that were RoundUp-resistant and made a lot of money off of it, which many people find problematic.

There are a few other problems that people have with GMO’s.  Natural Revolution.org writes, “In sum, genetic engineering artificially combines genes from different species and forcibly inserts them into unknown and random locations on the host genome. The procedure, which disrupts the precise orchestration of thousands of genes that has evolved over millennia in the normal plant’s genome, is highly mutagenic. (We now know that genes, like nutrients, do not work singly, but as part of highly integrated networks.) Plus it introduces bacterial genes for drug resistance along with strong promoters to express the foreign proteins at high levels in all parts of the plant.”

What does science say?

Genetically modification is actually not a new concept.  Humans have been altering the DNA sequence of plants and animals through selective breeding for thousands of years.  Selective breeding is when people identify a certain trait that is desirable, and then they breed other individuals in that species with the individual that possesses that trait, in order to spread that trait to the rest of the population.  The end result is similar to genetic modification: humans change the proportions of traits in a population.

Natural Revolution.org seems to use a lot of rhetoric in their post, such as genes are being “forcibly inserted.”  When genetic modification is done correctly, and it has been done correctly, the results are exactly what we want to see.  It can be problematic when genetic modification is not done correctly, but when it is, the results are incredibly beneficial.  For example, vitamin A deficiency in some developing countries is a huge problem.  Therefore, using genetic modification, scientists developed golden rice, which is rice that has been modified to include beta-carotene.  This gives the golden rice more vitamin A to combat these nutritional problems.  Another example is biofuels; sorghum can be modified to weaken the cells wells to make it easier to break down for biofuels, which makes biofuels even more efficient.  Finally, some of the most widely known benefits of GMO’s are benefits to agriculture.  Because genes for insecticide and pesticides are inserted into genes, it reduces the use of pesticides on the outside, which can seep into the soil and cause problems with surface runoff.  GMO’s have a similar benefit with fertilizer and water; if we can genetically modify plants to be drought-resistant or to need less fertilizer, we can solve many pressing global issues.

Common Misconceptions

(1) Round-Up is toxic and can harm humans.  Round-Up is a chemical called glyphosate, which is a polar substance.  This means that the molecule has areas of positive charge and areas of negative charge.  However, when toxic chemicals build up (or bioaccumulate) in our bodies, they do so in fatty cells, which are very nonpolar.  When it comes to polarity, like dissolves like, so glyphosate would not bioaccumulate in these fatty cells due to polarity.  Therefore, it is, for the most part, simply excreted through urine and therefore does not harm humans.

Obviously, ingesting chemicals can be harmful, but this is more an issue with the use of fertilizers and pesticides in general, rather than an issue with genetically modified organisms.  Many argue that our diversity, key species, and the soil is harmed by herbicides or pesticides, but this is not because of GMO’s, but a wider problem.

(2) Joining plant genes with genes from organisms is not natural.  This may be true, this would never happen in nature.  However, the genetic makeup of DNA is exactly the same between these domains (a nucleotide guanine in one is the same as a guanine in the other).  Additionally, it is important to remember that these genetic materials are still related, just very distantly.  Since all organisms are derived from one common ancestor, plant and bacterial genetics are related.

It is important to keep in mind that genetic modification CAN be harmful if done incorrectly.  However, when done carefully and by experts, it can be a powerful tool for preserving our environment, reducing our destruction of ecosystems, and helping us feed a growing world population.

Please feel free to ask questions in the comments and I will try to do some research and answer them!

Citations:

http://www.csiro.au/Outcomes/Food-and-Agriculture/WhatIsGM.aspx

http://naturalrevolution.org/gmo-resources/the-good-bad-and-ugly-about-gmos/

http://www.npr.org/blogs/thesalt/2013/03/07/173611461/in-a-grain-of-golden-rice-a-world-of-controversy-over-gmo-foods

http://npic.orst.edu/factsheets/glyphotech.html#chem

Short Addendum to Rationale

I would just like the mention that, while I believe that everyone should be scientifically literate in a most basic sense and hopefully this will help with that, it is not just science.  Making decisions in life requires a knowledge of economics, political science, history, mathematics, etc., and, especially in regard to making political decisions, everyone should have an understanding of the theories and facts behind decisions they make.  I just happen to know more about science, so this blog is about the science aspect of that.

Rationale

Science has the potential to explain such fascinating mysteries of life, and yet science also has a reputation for being relatively complex and, often, difficult to understand.  Many pressing issues that come up during elections or are everyday decisions we have to make involve, and require, a knowledge of science that many people do not have and yet are asked to form opinions about all the time.  Everyone wishes to form educated opinions about these issues, but the information to truly form unbiased opinions about science is often inaccessible.  The intent of this website is to take some of these science issues and decisions and elucidate some of the truth behind them.

Here are a few struggles I encountered when deciding to write this blog.  The first is simply that truths as absolutes either do not exist or are incredibly hard to find.  While there are plenty of documentaries and essays written on the effect of nuclear power, almost all of them use rhetoric and some form of data manipulation or exaggeration (not in the academically dishonest way, but simply in the sense that they place emphasis on the data they feel is most important, but it makes it more difficult to see both sides of the issue).  These problems make the scientific truths very difficult to decipher from all the bias that everyone introduces to anything they create.  I plan to do my best to provide both sides of an issue, but I will place emphasis on where the scientific truths lie.  For example, there are definitely two sides to the global warming debate, but scientific evidence and “truth” lie overwhelmingly to one side (I am sure I will elaborate on this more in a later post).  However, I will, for the most part, post citations to where I find my information and try to get the vast majority from legitimate, peer-reviewed scientific journals.  I’m sure I will also post more on the epistemology of this blog, particularly with regard to the peer review process, which is so often criticized.

There is an art to maneuvering data manipulation, and unfortunately this is not a skill widely taught in schools (although it definitely should be).  Anyone more interested in learning about how data manipulation works within our government, the media, and how to combat it, I highly recommend the book Proofiness by Charles Seife.  I am also sure that I will reference this book many times.

Additionally, combating scientific mistruths (attempting to use science to prove things that are not true) can be accomplished by following “The 10 Commandments of Logic” found below (found from the “I F***ing Love Science” Facebook page).

Thank you for reading this slightly lengthy introduction, and I look forward to discussing scientific issues!