Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts

Sunday, April 5, 2015

Top Geneticist Rejects the "Junk DNA" viewpoint




Oh look! I have in my hand the most up-to-date book available,
on Mobile DNA. Its by the world's leading expert on that topic.

Oh oh, he's not an ID guy. He's not a creationist.
OMG he's not even a Christian or Jew, or muslim.

The title is hilariously "Mobile DNA", by H.H. Kazazian, (2012, FT Press).


We'd better check his credentials:
We wouldn't want any 'unscientific' amateurs sneaking in,
misrepresenting themselves and taking credit for BAs in philosophy,
or PhDs in religion here:


Hmmm. lets see:

finished his M.D. degree at Johns Hopkins University School of Medicine.

Interned in Pediatrics at University of Minnesota Hospital.

Returned to Johns Hopkins for a Fellowship in Genetics,

Then Trained in molecular biology at the NIH.

Rejoined the Faculty at Johns Hopkins.

Rose to full professorship there in 1977.

Became Director of the Center for Medical Genetics (Johns Hopkins) 1988.

Spent 25 years on the John Hopkins Faculty.

Recruited to University of Pennsylvania School of Medicine, as
Chair of the Dept. of Genetics in 1994.

Remained as Seymour Grey Professor of Molecular Medicine in Genetics till 2010.

Returned to Johns Hopkins in July 2010.

Heavily involved in molecular genetic research for the past 20 years
specializing in mammalian and human transposable elements, "jumping genes".

Personally characterized much of the variation in the cluster of genes
involved in production of the beta chain of human hemoglobin.

His work led to the nearly complete characterization of the mutations
causing the Beta-thalassemias, common anemias in malaria regions.

Received many honours for his research, most notably the
2008 William Allan Award, the top honour of the
American Society of Human Genetics.


Well, what does he say about Junk DNA?


"...most genes are broken up by sections of DNA called introns
that need to be removed at the RNA stage in order for the genes
to function. ...the protein-coding regions of the genes make up
a very small fraction of mammalian genomes.
...In the late 1970s, introns were found...
Soon we knew that introns were much larger than protein-coding regions,
then called exons.
The DNA between the genes was thought to be functionless,
and was called "junk DNA" (Orgel and Crick, 1980).
However, now we know that introns make up about 30% of human
and mammalian genomes, and exons only encode between 1 and 2%
of the human genome (Lander et al., 2001).
What a comedown for the protein-encoding regions!
Thus over 98% of human DNA had been dismissed as "junk".

Transposable elements were then found, and this active mobile DNA
along with the remnants is now known to account for at least 50%
of human genomic DNA. Both the relatively few presently mobile
sequences, and the many remnants of old events are now
demonstrating function.

...evident in the many ways mobile DNA can modify the genome over evolutionary time.
It can also be co-opted for useful purposes...
Moreover, DNA encoding small RNAs of different types and functions
has been discovered amidst the "junk". Enhancer sequences at great
distances from the genes upon which they act are being found continually.
...
The bottom line is that "junk" DNA is gradually being eroded away as
function is found for a greater and greater fraction of the genomic DNA
."


- Mobile DNA, pp. 1-3

His comfortable use of "evolutionary" makes clear he is an evolutionist,
as well as one of the top experts in human DNA.

Thursday, September 13, 2012

Monday, September 3, 2012

Attacks on Irreducible Complexity Deconstructed (4)

The Court of ...Science?  ....


The next step the narrator takes,
actually takes us right out of the realm of scientific investigation,
into the world of political posturing and nonsense.




Of course when religious apologists,  New-Agers, Conspiracy Theorists (does anyone actually self-identify as this?), or Creationists, Intelligent-Design proponents, and Irreducible Complexity advocates dare to use the standard debating techniques, such as:


(1)  Ad Hominem - attacking the person who is the source of an idea.

(2)  Appeals to Numbers - suggesting that the majority is always right.

(3)  Appeal to Authority - what the experts / authorities say must be followed.
...whenever opponents use these popular tactics,
they are shot down mercilessly and exposed,
mainly because "such methods of winning arguments are
unscientific."

Secondly, everybody who has ever had experience in a courtroom (in ANY country),
knows that courtrooms are literally full of lies, nonsense, injustice, and obfuscation.

Only a fool would today claim that "truth" is best resolved, or in fact resolved at all in a modern courtroom.   It matters not whether the case
is big or small, rich or poor, intelligent or moronic.

Courtrooms are of course run by lawyers
, and without prejudice,
lawyers are human beings, most of whom are motivated mainly by money,
secondly by political passion, and perhaps as a limping third, justice and truth.
Or at least community justice, or perhaps pragmatism.

Yet when a court rules in favour of the cause of Evolution, we are suddenly
treated to the most amazing fairy-story of all:

Courts are now the "ultimate" arbiters of truth:
Perhaps even the best discoverers and establlishers of scientific truth.




Suddenly, the lawyers have become our heroes, accurately dissecting the bitter pill of Intelligent Design, to discover the horror of Creationism,
masquerading as 'science' and daring to "infect our children".

Please.

If a person born anytime during the post-war baby-boom knows anything,
he knows this is pure horse-manure.


Attacks on Irreducible Complexity Deconstructed (3)

Three Blind Mice

Next the video-maker runs through three examples used by Irreducible Complexity advocates;

(1) The Eye,

(2) The bombadier Beetle,

(3) The Mouse-Trap
example of Michael Behe.

We skip the bombadier Beetle example, because frankly, its nowhere near the required complexity in the first place, to qualify as an example.
In this the narrator is probably right, not about its evolution, which begs the question, but that its a FAIL as an example of Irreducible Complexity.

The Mouse-trap example is more interesting, but as far as we and the narrator are concerned, its not a living creature, and probably not an example of Irreducible Complexity either.

Nonetheless, without a perfect or complete scientific methodology, we can still be 99% sure that the mouse-trap was not a natural formation, but the result of an Intelligent Designer. There is little point in arguing about this.

We know the mouse-trap is a Designed Object for a number reasons, all of which can be scientifically investigated, analyzed, and expressed, provided we want to bother to put in the time.

Its not only 'complexity' that results in a good case for Intelligent Design, but a number of factors, including circumstantial evidence. For instance:

(1) The mouse-trap is made of iron wire, something we can already identify as man-made.

(2) It has a mechanical spring, the material, size and shape of which never occurs in the natural world, outside of man's activity.

(3) It has a logo painted on it, identifying the company and where it was made.

This brings up the problem of the huge hole in the video's narrative.
The narrator makes no proper distinction between Intelligent Design and Irreducible Complexity. He simply lumps everthing together under "Creationism", and labels that a 'religious ideology'.

He has no excuse, for later in the video he is quite careful about the definitions and philosophical implications of Irreducible Complexity.

Since he doesn't give Intelligent Design anywhere near the same care and attention, its obvious he's not being scientific, or even thorough:
He's being a propagandist.

Yet to any real scientist, the two ideas are quite clearly distinct,
and this distinction is crucial to fields such as cryptology and military surveillance.


The narrator makes an important point following the discussion of the mouse-trap here:




Thus the narrator is quite capable of making the crucially important distinction between LIVING things and NON-Living things.

But what is the real significance of this?

The whole original inquiry is based on this critical observation:

Living Things Don't follow the 'natural laws'
that utterly fix and determine the behavior of dead things.


(1) Living things make copies of themselves. Dead things don't.

(2) Living things evolve complex information systems and machinery. Dead things DON'T.

(3) Living things operate AGAINST both thermodynamic and Informational Laws of Entropy. Dead things don't!

Its futile to insist that Living things follow the same physical and chemical laws as dead things, which is an underlying 'text' of atheistic evolution,
when the whole point of real science is to investigate why they DON'T.

To miss this is to misdirect what science actually is, and what the real business of scientific investigation should be.

Saturday, August 25, 2012

Sunday, August 19, 2012

Bogus Abiogenesis

I'm quoting the narrative from this corny Youtube video
for pure entertainment value.

Its really quite the load of B.S.:

I'll be analysing it shortly:

___________________________________________

 The Origin of Life Made Easy  
  
When Bill O'Reilly asked Kirk Cameron to give his best shot in
proving the existence of God this is what he said:

"The fact that there's a painting proves there must be a painter;
The human body proves there must be a designer because of its complexity  and because of the information we can see down at the DNA level"

The problem for fundamentalists like Cameron is that this argument can be too easily  flattened.  In this video I want to show what scientists have actually deduced about the origins of life, so let's start by putting the 'artist and painting' myth to rest.



Why can't paintings paint themselves? 
Simple: Because they're made of chemicals that can't replicate themselves.
Living matter on the other hand does contain a chemical that can replicate itself. Even if God made DNA he doesn't need to intervene every time animals mate. The DNA does the job on its own. So the real question is, how did DNA appear?

How did living matter come from non living sludge?
Here again fundamentalists need to drop a common argument that seems to be based  on complete ignorance of current scientific hypotheses, which is this:
"Scientists believe life just popped out of nowhere."

Of course that's not what scientists believe.
Life popping out of nowhere is no better a theory
than life popping out of the hand of a deity.
So what do scientists believe about the origin of life?

Let's take this step-by-step: 
The first step involves looking at the primordial earth 4.7 billion years ago.




There it is, very wet, very warm and with an atmosphere composed of all sorts of gases;
 hydrogen, hydrogen cyanide, methane, and ammonia among them.





Step 1: Formation of Nucleotides


DNA is a long chain molecule made from just four different types of nucleotide, so the first question is where did the nucleotides come from. 



In 1961 a researcher called Huan Oto left hydrogen cyanide and ammonia
to stew in an aqeous solution in his laboratory under conditions
very similar to those that prevailed on the primordial earth.


Left alone the solution produced adenine, one of the four nucleotide bases that make up DNA.



  To make a complete nucleotide these bases need to gain a sugar called Ribose, and a group of phosphates.





Biochemist think they know how the phosphate group formed.
They are now trying to find out how the ribose is attached.



 
Step 2: Nucleotides to Polynucleotides

------------------------- >

Once nucleotides formed, the next step was to join together to make chains called polynucleotides.


 

 In the 1980s researchers found that a clay called montmorillonite, which was abundant on the primordial seafloor and in hot pools of water on land, is the perfect catalyst for this process.



 

Step 3:  Polynucleotides to RNA

 

Some of these long polynucleotide chains like ribonucleic acid or RNA are able to make copies of themselves.  The copies aren't always perfect: mistakes creep in.  But some imperfectly copied molecules would have been better adapted to the environment than others.

These successful molecules continue to replicate and pass on their traits,  while weaker or less well adapted molecules would have broken apart.

Step 4:  RNA to Protocells

As RNA molecules replicated themselves, they shared their environment with other chemicals that thrive in montmorillonite clay.




One group, called lipids, have a natural tendency to clump together, to form spherical structures called mycells.




RNA molecules that attracted these lipids,












would therefore find themselves protected inside a mycell membrane.




Because they were better protected, they better survived and replicated
more successfully.  There you have the first primitive cells.  They looked nothing like the complex cells we have today for a very good reason:  Over 3.7 billion years they've evolved. 




I'll tackle the subject of evolution in another video.




 
Step 5:  RNA to DNA

Over 100s of millions of years RNA grew more complex. 




The single-strand became a double-strand and the better-adapted DNA molecule evolved.



One of the differences between RNA and DNA is that DNA needs proteins to replicate itself.

Proteins are made of amino acids, which are often called the building blocks of life.




 
Step 6: Formation of Amino Acids

So where did the first ones come from?
No, there was no need for God:



----- >
     

 

A number of experiments using montmorillonite have produced not only amino acids, but long chains of amino acids called polypeptides.

 


Montmorillonite it turns out, is a natural breeding ground
for all kinds of complex organic chemicals.





It has to be said that this research is in its infancy and current hypotheses are nowhere near as solid as the Theory of Evolution,  which has been around for 150 years, and has overwhelming evidence to support it.

But the reality is a far cry from the idea that scientists believe life popped out of nowhere. If God did indeed create life then where did he come in? Step one?  - step two?  and why?  If the chemical process can happen on its own, why would God intervene at all?

Before I go I just want to look at a couple of other hoary old arguments that are being used, and which also show a complete ignorance of science.

"It's impossible for simple chemicals to form more complex chemicals
without intvervention."

Just because creationist websites like to pass this myth around doesn't make it true. We know it's not true.  Left alone, organic chemicals can and do polymerize, to form longer more complex chemicals.

"But this goes against the Law of Thermodynamics."

Oh that sad argument: The fact is that the natural formation of replicating chemicals doesn't conflict with any of the laws of thermodynamics.
People who make that argument need to read the law, because I suspect most of them have never done so and are just mindlessly repeating an urban myth, that's already been debunked.

As I've said we still have a lot more to learn about this process.
Researchers know that there are many more intermediate steps that we haven't  yet discovered. 

And when all of them are found, there will still be fundamentalists around
 to say, "Ah, but you can't prove that this is how life started on earth."
No, we probably never will.  But what we can say is if there's a natural process by which the first replicating molecules appeared on earth,  then we don't need to invent Gods, goddesses and other invisible deities to explain it.  Ultimately this isn't a guessing game, it's a detective trail.'  
 
_____________________________________
End of video text


-- Uploaded by potholer54 on Nov 13, 2008         

The video explains current ideas as to how life might have originated on Earth. The idea that inorganic mud can miraculously turn into cells is a claim made in the Bible and the Qu'ran, not science. What biologists are trying to do is understand how carbon-based chemicals combine to form nucleotides, the building blocks of replicating chemicals. The chemistry is complex, but it's starting to be understood, and it's not magical.

Please also see The Origin of Life - Abiogenesis by cdk007
which gives an excellent description on the latest hypotheses about cell formation. 
  
-----------------------------------------------
Okay, there's the text with some snaps from the video.

I'll critique it as time permits.